The following packages were found for maintainer: bacon@NetBSD.org
archivers/libaec [CURRENT] Adaptive entropy coding library
biology/biolibc-tools [CURRENT] High-performance bioinformatics tools based on biolibc
wip/ad2vcf [CURRENT] Add allelic depth info from a SAM stream to a VCF file
wip/centrifuge [CURRENT] Novel microbial classification engine
wip/smithwaterman [CURRENT] Smith-waterman-gotoh alignment algorithm
wip/canu [CURRENT] Single molecule sequence assembler for genomes large and small
biology/fastp [CURRENT] Ultra-fast all-in-one FASTQ preprocessor
biology/canu [CURRENT] Single molecule sequence assembler for genomes large and small
biology/samtools [CURRENT] Tools for manipulating sequence alignment maps
wip/munge [CURRENT] Authentication service for creating and validating credentials
biology/atac-seq [CURRENT] Core tools needed for ATAC-Seq analysis
www/webbrowser [CURRENT] Proxy script for launching best available web browser
wip/structure [CURRENT] Multi-locus genotype data to investigate population structure
devel/simde [CURRENT] Header-only library for SIMD intrinsics
wip/libgtextutils [CURRENT] Gordon text utilities
devel/libgtextutils [CURRENT] Gordon text utilities
math/basic-stats [CURRENT] Command-line tool to perform basic statistics on tabular data
biology/kallisto [CURRENT] Quantify abundances of transcripts from RNA-Seq data
biology/htslib [CURRENT] C library for high-throughput sequencing data formats
wip/vcf2hap [CURRENT] Generate .hap file from VCF for haplohseq
wip/plasm [CURRENT] Portable Assembler
wip/fasda [CURRENT] Fast and simple differential analysis
biology/cdhit [CURRENT] Clustering and comparing protein or nucleotide sequences
biology/generand [CURRENT] Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
biology/hisat2 [CURRENT] Alignment program for mapping next-generation sequencing reads
biology/vsearch [CURRENT] Versatile open-source tool for metagenomics
biology/fastx-toolkit [CURRENT] CLI tools for Short-Reads FASTA/FASTQ files preprocessing
devel/libxtend [CURRENT] Miscellaneous functions to extend libc
wip/stacks [CURRENT] Software pipeline for building loci from short-read sequences
wip/rsem [CURRENT] RNA-Seq by Expectation-Maximization
wip/ddocent [CURRENT] Bash pipeline for RAD sequencing
wip/gmap [CURRENT] Genomic Mapping and Alignment Program for mRNA and EST Sequences
wip/R-optparse [CURRENT] Command Line Option Parser
wip/linux-ukbgene [CURRENT] Tool for accessing UK Biobank data
wip/famsa [CURRENT] Algorithm for large-scale multiple sequence alignments
wip/brain-mesh-builder [CURRENT] Surface mesh building based on 3-dimensional image stacks
wip/muscle [CURRENT] MUltiple Sequence Comparison by Log-Expectation
wip/py-macs2 [CURRENT] Algorithm for identifying transcription factor binding sites
wip/samtools [CURRENT] Tools for manipulating sequence alignment maps
wip/packmol [CURRENT] Pack molecules in defined regions of space
wip/trinity [CURRENT] Assembles transcript sequences from Illumina RNA-Seq data
wip/rainbow [CURRENT] Short reads clustering and local assembly
wip/cereal [CURRENT] C++11 library for serialization
wip/igv [CURRENT] Visualization tool for genomic datasets
wip/vcf-split [CURRENT] Split a multi-sample VCF into single-sample VCFs
wip/prodigal [CURRENT] Prokaryotic Dynamic Programming Genefinding Algorithm
wip/cut-and-run [CURRENT] Split a text file into segments and process in parallel
wip/ncbi-blast+ [CURRENT] NCBI implementation of Basic Local Alignment Search Tool
wip/metal [CURRENT] Meta-analysis of genomewide association scans
wip/detab [CURRENT] Replace tabs with spaces in a text file
wip/fastool [CURRENT] Simple and quick FastQ and FastA tool for file reading and conversion
wip/auto-admin [CURRENT] Portable tools for automating systems management
wip/py-bcbio-gff [CURRENT] Read and write Generic Feature Format (GFF) with Biopython integration
wip/py-dna-features-viewer [CURRENT] Python library to visualize DNA features, e.g. GenBank or Gff files
wip/py-macs3 [CURRENT] Peak caller aimed at transcription factor binding sites
wip/libpare [CURRENT] Pointer Array Regular Expressions
wip/fastq-trim [CURRENT] Lightening fast sequence read trimmer
wip/fasttree [CURRENT] Approximately-maximum-likelihood phylogenetic trees from alignments
wip/globalprotect-openconnect [CURRENT] OpenConnect GUI for GlobalProtect protocol
wip/fastp [CURRENT] Ultra-fast all-in-one FASTQ preprocessor
wip/microsynteny-tools [CURRENT] Tools for exploring microsyntenic differences among species
wip/py-capturer [CURRENT] Easily capture stdout/stderr of the current process and subprocesses
wip/jellyfish2 [CURRENT] Fast, memory-efficient counting of k-mers in DNA
wip/slclust [CURRENT] Single-linkage clustering with Jaccard similarity
wip/tabixpp [CURRENT] C++ wrapper to tabix indexer
wip/atac-seq [CURRENT] Core tools needed for ATAC-Seq analysis
wip/subread [CURRENT] High-performance read alignment, quantification and mutation discovery
wip/hisat2 [CURRENT] Alignment program for mapping next-generation sequencing reads
wip/pear [CURRENT] Memory-efficient and highly accurate pair-end read merger
wip/py-graph-tool [CURRENT] Python module for manipulation and statistical analysis of graphs
wip/xssp [CURRENT] Software for creating DSSP and HSSP files
wip/spcm [CURRENT] Simple, portable cluster management
wip/ufc [CURRENT] Unified framework for finite element assembly
wip/intervaltree [CURRENT] Minimal C++ interval tree implementation
wip/py-rdfextras [CURRENT] Collection of packages providing extras based on RDFLib 3
wip/wip-tools [CURRENT] Tools for developing wip packages
wip/yaggo [CURRENT] Generate command line parser using getopt_long
wip/p5-transdecoder [CURRENT] Identify candidate coding regions within transcript sequences
wip/py-pysam [CURRENT] Python module for reading, manipulating and writing genomic data sets
wip/fbsd2pkg [CURRENT] Convert a FreeBSD port framework to a pkgsrc package
wip/mst-bench [CURRENT] Maximum sustainable throughput benchmark
wip/bio-mocha [CURRENT] Bcftools plugin for mosaic chromosomal alteration analysis
wip/vsearch [CURRENT] Versatile open-source tool for metagenomics
wip/lpjs [CURRENT] Lightweight, Portable Job Scheduler
wip/filevercmp [CURRENT] Filevercmp function as in sort --version-sort
wip/py-rdflib340 [CURRENT] Python library for RDF manipulation
wip/twintk [CURRENT] Terminal Windows Toolkit
wip/fastx-toolkit [CURRENT] CLI tools for Short-Reads FASTA/FASTQ files preprocessing
wip/rna-seq [CURRENT] Core tools needed for RNA-Seq analysis
wip/seqtk [CURRENT] Tool for processing sequences in FASTA/FASTQ format
wip/webbrowser [CURRENT] Proxy script for launching best available web browser
wip/py-htseq [CURRENT] Python library to facilitate programmatic analysis of sequence data
wip/haplohseq [CURRENT] Identify regions of allelic imbalance
wip/py-anvio [CURRENT] Analysis and visualization platform for omics data
wip/libzeep [CURRENT] Make it easy to create SOAP servers
wip/peak-classifier [CURRENT] Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
wip/auto-dev [CURRENT] Tools for automating code development and documentation
wip/papp [CURRENT] Assembly Preprocessor
wip/htslib [CURRENT] C library for high-throughput sequencing data formats
wip/gffread [CURRENT] GFF/GTF format conversions, filtering, FASTA extraction, etc
wip/basic-stats [CURRENT] Command-line tool to perform basic statistics on tabular data
wip/libxtend [CURRENT] Miscellaneous functions to extend libc
wip/plink2 [CURRENT] Whole genome association analysis toolset
wip/biolibc [CURRENT] Low-level high-performance bioinformatics library
wip/bowtie2 [CURRENT] Ultrafast, memory-efficient short read aligner
wip/fsom [CURRENT] Tiny C library for managing SOM (Self-Organizing Maps) neural networks
wip/p5-trimgalore [CURRENT] Wrapper around Cutadapt and FastQC for adapter and quality trimming
wip/docviewer [CURRENT] Generic command to automatically select a document viewer
wip/generand [CURRENT] Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
wip/biolibc-tools [CURRENT] High-performance bioinformatics tools based on biolibc
biology/py-macs2 [CURRENT] Algorithm for identifying transcription factor binding sites
biology/bwa [CURRENT] Map low-divergent sequences against a large reference genome
biology/trimmomatic [CURRENT] Flexible read trimming tool for Illumina NGS data
biology/fastqc [CURRENT] Quality control tool for high throughput sequence data
biology/ad2vcf [CURRENT] Add allelic depth info from a SAM stream to a VCF file
biology/vcf2hap [CURRENT] Generate .hap file from VCF for haplohseq
biology/igv [CURRENT] Visualization tool for genomic datasets
biology/peak-classifier [CURRENT] Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
biology/fasda [CURRENT] Fast and simple differential analysis
wip/ape [CURRENT] Another Programmers Editor
biology/stacks [CURRENT] Software pipeline for building loci from short-read sequences
biology/ncbi-blast+ [CURRENT] NCBI implementation of Basic Local Alignment Search Tool
biology/bowtie2 [CURRENT] Ultrafast, memory-efficient short read aligner
biology/fastq-trim [CURRENT] Lightening fast sequence read trimmer
biology/plinkseq [CURRENT] C/C++ library for working with human genetic variation data
wip/kallisto [CURRENT] Quantify abundances of transcripts from RNA-Seq data
wip/bwa [CURRENT] Map low-divergent sequences against a large reference genome
wip/plink [CURRENT] Whole genome association analysis toolset
wip/isa-l [CURRENT] Intel(R) Intelligent Storage Acceleration Libray
biology/seqtk [CURRENT] Tool for processing sequences in FASTA/FASTQ format
sysutils/auto-admin [CURRENT] Portable tools for automating systems management
wip/npmount [CURRENT] Command line tool for non-privileged [un]mount
wip/qmediamanager [CURRENT] GUI tool for managing removable media
wip/devpub-mount [CURRENT] NetBSD devpubd-based automounter
wip/desktop-installer [CURRENT] Quickly configure a NetBSD desktop system
sysutils/devpub-mount [CURRENT] NetBSD devpubd-based automounter
sysutils/npmount [CURRENT] Command line tool for non-privileged [un]mount
biology/chip-seq [CURRENT] Core tools needed for ChIP-Seq analysis
sysutils/desktop-installer [CURRENT] Quickly configure a NetBSD desktop system
sysutils/qmediamanager [CURRENT] GUI tool for managing removable media
wip/fuse-exfat [CURRENT] FUSE file-system and utilities for exFAT file systems
wip/py-multiqc [CURRENT] Aggregate bioinformatics analysis reports across samples and tools
wip/stringtie [CURRENT] Transcript assembly and quantification for RNA-seq
wip/rna-star [CURRENT] Spliced Transcripts Alignment to a Reference
biology/rna-star [CURRENT] Spliced Transcripts Alignment to a Reference
devel/py-capturer [CURRENT] Easily capture stdout/stderr of the current process and subprocesses
devel/py-coloredlogs [CURRENT] Colored terminal output for Pythons logging module
archivers/py-lzstring [CURRENT] LZ-based in-memory string compression
devel/py-verboselogs [CURRENT] Extend Python logging module to add the log levels
wip/py-lzstring [CURRENT] LZ-based in-memory string compression
devel/py-rich-click [CURRENT] Format click help output nicely with rich
math/py-colormath [CURRENT] Module that spares the user from directly dealing with color math
graphics/py-spectra [CURRENT] Color scales and color conversion made easy for Python
biology/py-multiqc [CURRENT] Aggregate bioinformatics analysis reports across samples and tools
wip/py-spectra [CURRENT] Color scales and color conversion made easy for Python
textproc/py-humanfriendly [CURRENT] Human friendly output for text interfaces using Python
biology/stringtie [CURRENT] Transcript assembly and quantification for RNA-seq
biology/bcftools [CURRENT] Tools for manipulating BCF and VCF variant call files
wip/sra-tools [CURRENT] NCBIs toolkit for handling data in INSDC Sequence Read Archives
biology/sra-tools [CURRENT] NCBIs toolkit for handling data in INSDC Sequence Read Archives
biology/rna-seq [CURRENT] Core tools needed for RNA-Seq analysis
sysutils/runas [CURRENT] Wrapper around su for running a command as another user
wip/gcta [CURRENT] Genome-wide Complex Trait Analysis
wip/bifrost [CURRENT] Parallel construction, indexing and querying of de Bruijn graphs
biology/py-bcbio-gff [CURRENT] Read and write Generic Feature Format (GFF) with Biopython integration
biology/py-dna-features-viewer [CURRENT] Python library to visualize DNA features, e.g. GenBank or Gff files
biology/microsynteny-tools [CURRENT] Tools for exploring microsyntenic differences among species
wip/py-cython-legacy [CURRENT] C-Extensions for Python
math/armadillo [CURRENT] C++ linear algebra library
wip/py-pybigwig [CURRENT] Python access to bigWig files using libBigWig
wip/chip-seq [CURRENT] Core tools needed for ChIP-Seq analysis
wip/py-cykhash [CURRENT] Cython equivalent to khash-sets/maps
biology/py-macs3 [CURRENT] Peak caller aimed at transcription factor binding sites
devel/py-cykhash [CURRENT] Cython equivalent to khash-sets/maps
wip/biostar-tools [CURRENT] Meta-package for Biostar Handbook tools
wip/bedtools [CURRENT] Swiss army knife for genome arithmetic
wip/py-pyaml-env [CURRENT] Provides yaml file parsing with environment variable resolution
wip/runas [CURRENT] Wrapper around su for running a command as another user
wip/bolt-lmm [CURRENT] Statistics for testing association between phenotype and genotypes
wip/fastahack [CURRENT] Utilities for indexing and sequence extraction from FASTA files
wip/parafly [CURRENT] Process the commands in parallel on a single server
wip/vcftools [CURRENT] Tools for working with VCF genomics files
wip/py-ete3 [CURRENT] Python Environment for (phylogenetic) Tree Exploration
wip/py-eggnog-mapper [CURRENT] Fast functional annotation of novel DNA or protein sequences
wip/antlr [CURRENT] ANother Tool for Language Recognition
wip/py-hostlist [CURRENT] Manage SLURM host lists
wip/py-dnaio [CURRENT] Read and write FASTQ and FASTA files
wip/slurm-wlm-devel [CURRENT] Simple Linux Utility for Resource Management
wip/gemma [CURRENT] Genome-wide Efficient Mixed Model Association
wip/R-getopt [CURRENT] C-Like getopt Behavior
wip/fastaunique [CURRENT] Sort and uniq fasta files
wip/wgrib2 [CURRENT] Tools for managing GRIB weather data files
wip/jellyfish [CURRENT] Fast, memory-efficient counting of k-mers in DNA
wip/p5-IPC-Open3-Simple [CURRENT] Simple alternative to IPC::Open3
wip/readseq [CURRENT] Read and reformat biosequences, Java command-line version
wip/pkg-dev [CURRENT] Scripts to automate common tasks in pkgsrc development
wip/pooler [CURRENT] Optimise DNA sequencing primer-set combinations
wip/R-mpfr [CURRENT] Multiple Precision Floating Point Arithmetic for R
wip/bpcscripts [CURRENT] Gast Illumina processing
biology/biolibc [CURRENT] Low-level high-performance bioinformatics library
biology/plink [CURRENT] Whole-genome association analysis toolset
biology/gffread [CURRENT] GFF/GTF format conversions, filtering, FASTA extraction, etc
wip/mcl [CURRENT] Fast and scalable unsupervised cluster algorithm for graphs
wip/epacts [CURRENT] Efficient and Parallelizable Association Container Toolbox
biology/bedtools [CURRENT] Swiss army knife for genome arithmetic
biology/vcf-split [CURRENT] Split a multi-sample VCF into single-sample VCFs
wip/udunits2 [CURRENT] Library for manipulating units of physical quantities
devel/py-xopen [pkgsrc-2017Q4] Open compressed files transparently
biology/bwa [pkgsrc-2017Q4] Map low-divergent sequences against a large reference genome
devel/py-xopen [pkgsrc-2018Q1] Open compressed files transparently
parallel/slurm [pkgsrc-2018Q1] Simple Linux Utility for Resource Management
textproc/man2html [pkgsrc-2018Q1] Convert nroff(1) man pages to HTML
biology/bwa [pkgsrc-2018Q1] Map low-divergent sequences against a large reference genome
security/munge [pkgsrc-2018Q1] Authentication service for creating and validating credentials
biology/samtools [pkgsrc-2018Q2] Tools for manipulating next-generation sequencing data
parallel/slurm-wlm [pkgsrc-2018Q2] Simple Linux Utility for Resource Management
parallel/ganglia-monitor-core [pkgsrc-2018Q2] Ganglia cluster monitor, monitoring daemon
textproc/man2html [pkgsrc-2018Q2] Convert nroff(1) man pages to HTML
biology/bwa [pkgsrc-2018Q2] Map low-divergent sequences against a large reference genome
security/munge [pkgsrc-2018Q2] Authentication service for creating and validating credentials
devel/py-xopen [pkgsrc-2018Q2] Open compressed files transparently
biology/ncbi-blast+ [pkgsrc-2018Q2] NCBI implementation of Basic Local Alignment Search Tool
biology/htslib [pkgsrc-2018Q2] C library for high-throughput sequencing data formats
textproc/man2html [pkgsrc-2018Q3] Convert nroff(1) man pages to HTML
parallel/ganglia-monitor-core [pkgsrc-2018Q3] Ganglia cluster monitor, monitoring daemon
devel/py-xopen [pkgsrc-2018Q3] Open compressed files transparently
biology/ncbi-blast+ [pkgsrc-2018Q3] NCBI implementation of Basic Local Alignment Search Tool
parallel/slurm-wlm [pkgsrc-2018Q3] Simple Linux Utility for Resource Management
biology/bwa [pkgsrc-2018Q3] Map low-divergent sequences against a large reference genome
biology/trimmomatic [pkgsrc-2018Q3] Flexible read trimming tool for Illumina NGS data
biology/samtools [pkgsrc-2018Q3] Tools for manipulating next-generation sequencing data
biology/htslib [pkgsrc-2018Q3] C library for high-throughput sequencing data formats
security/munge [pkgsrc-2018Q3] Authentication service for creating and validating credentials
biology/trimmomatic [pkgsrc-2018Q4] Flexible read trimming tool for Illumina NGS data
security/munge [pkgsrc-2018Q4] Authentication service for creating and validating credentials
devel/py-xopen [pkgsrc-2018Q4] Open compressed files transparently
biology/ncbi-blast+ [pkgsrc-2018Q4] NCBI implementation of Basic Local Alignment Search Tool
biology/htslib [pkgsrc-2018Q4] C library for high-throughput sequencing data formats
biology/samtools [pkgsrc-2018Q4] Tools for manipulating next-generation sequencing data
biology/kallisto [pkgsrc-2018Q4] Quantify abundances of transcripts from RNA-Seq data
biology/bwa [pkgsrc-2018Q4] Map low-divergent sequences against a large reference genome
biology/stacks [pkgsrc-2018Q4] Software pipeline for building loci from short-read sequences
parallel/slurm-wlm [pkgsrc-2018Q4] Simple Linux Utility for Resource Management
parallel/ganglia-monitor-core [pkgsrc-2018Q4] Ganglia cluster monitor, monitoring daemon
textproc/man2html [pkgsrc-2018Q4] Convert nroff(1) man pages to HTML
security/munge [pkgsrc-2019Q1] Authentication service for creating and validating credentials
parallel/ganglia-monitor-core [pkgsrc-2019Q1] Ganglia cluster monitor, monitoring daemon
parallel/slurm-wlm [pkgsrc-2019Q1] Simple Linux Utility for Resource Management
math/arpack [pkgsrc-2019Q1] Library of subroutines to solve eigenvalue problems
devel/py-xopen [pkgsrc-2019Q1] Open compressed files transparently
biology/samtools [pkgsrc-2019Q1] Tools for manipulating next-generation sequencing data
devel/libctl [pkgsrc-2019Q1] Guile-based flexible control file library for scientific simulations
textproc/man2html [pkgsrc-2019Q1] Convert nroff(1) man pages to HTML
biology/trimmomatic [pkgsrc-2019Q1] Flexible read trimming tool for Illumina NGS data
devel/swig2 [pkgsrc-2019Q1] Simplified Wrapper and Interface Generator (version 2)
biology/ncbi-blast+ [pkgsrc-2019Q1] NCBI implementation of Basic Local Alignment Search Tool
biology/kallisto [pkgsrc-2019Q1] Quantify abundances of transcripts from RNA-Seq data
biology/stacks [pkgsrc-2019Q1] Software pipeline for building loci from short-read sequences
biology/hisat2 [pkgsrc-2019Q1] Alignment program for mapping next-generation sequencing reads
biology/bwa [pkgsrc-2019Q1] Map low-divergent sequences against a large reference genome
biology/canu [pkgsrc-2019Q1] Single molecule sequence assembler for genomes large and small
biology/plink [pkgsrc-2019Q1] Whole-genome association analysis toolset
biology/htslib [pkgsrc-2019Q1] C library for high-throughput sequencing data formats
biology/cdhit [pkgsrc-2019Q1] Clustering and comparing protein or nucleotide sequences
biology/plinkseq [pkgsrc-2019Q1] C/C++ library for working with human genetic variation data
biology/bcftools [pkgsrc-2019Q1] Calling and manipulating files VCF and BCF formats
biology/cdhit [pkgsrc-2019Q2] Clustering and comparing protein or nucleotide sequences
biology/ncbi-blast+ [pkgsrc-2019Q2] NCBI implementation of Basic Local Alignment Search Tool
biology/canu [pkgsrc-2019Q2] Single molecule sequence assembler for genomes large and small
biology/bcftools [pkgsrc-2019Q2] Calling and manipulating files VCF and BCF formats
parallel/ganglia-monitor-core [pkgsrc-2019Q2] Ganglia cluster monitor, monitoring daemon
biology/stacks [pkgsrc-2019Q2] Software pipeline for building loci from short-read sequences
parallel/slurm-wlm [pkgsrc-2019Q2] Simple Linux Utility for Resource Management
devel/libctl [pkgsrc-2019Q2] Guile-based flexible control file library for scientific simulations
biology/trimmomatic [pkgsrc-2019Q2] Flexible read trimming tool for Illumina NGS data
biology/plinkseq [pkgsrc-2019Q2] C/C++ library for working with human genetic variation data
biology/plink [pkgsrc-2019Q2] Whole-genome association analysis toolset
biology/fastp [pkgsrc-2019Q2] Ultra-fast all-in-one FASTQ preprocessor
security/munge [pkgsrc-2019Q2] Authentication service for creating and validating credentials
math/arpack [pkgsrc-2019Q2] Library of subroutines to solve eigenvalue problems
devel/swig2 [pkgsrc-2019Q2] Simplified Wrapper and Interface Generator (version 2)
archivers/libaec [pkgsrc-2019Q2] Adaptive entropy coding library
biology/samtools [pkgsrc-2019Q2] Tools for manipulating next-generation sequencing data
biology/kallisto [pkgsrc-2019Q2] Quantify abundances of transcripts from RNA-Seq data
biology/vsearch [pkgsrc-2019Q2] Versatile open-source tool for metagenomics
devel/py-xopen [pkgsrc-2019Q2] Open compressed files transparently
textproc/man2html [pkgsrc-2019Q2] Convert nroff(1) man pages to HTML
biology/htslib [pkgsrc-2019Q2] C library for high-throughput sequencing data formats
biology/bwa [pkgsrc-2019Q2] Map low-divergent sequences against a large reference genome
biology/hisat2 [pkgsrc-2019Q2] Alignment program for mapping next-generation sequencing reads
biology/bwa [pkgsrc-2019Q3] Map low-divergent sequences against a large reference genome
devel/swig2 [pkgsrc-2019Q3] Simplified Wrapper and Interface Generator (version 2)
math/arpack [pkgsrc-2019Q3] Library of subroutines to solve eigenvalue problems
parallel/ganglia-monitor-core [pkgsrc-2019Q3] Ganglia cluster monitor, monitoring daemon
biology/fastp [pkgsrc-2019Q3] Ultra-fast all-in-one FASTQ preprocessor
biology/canu [pkgsrc-2019Q3] Single molecule sequence assembler for genomes large and small
biology/samtools [pkgsrc-2019Q3] Tools for manipulating next-generation sequencing data
biology/ncbi-blast+ [pkgsrc-2019Q3] NCBI implementation of Basic Local Alignment Search Tool
parallel/slurm-wlm [pkgsrc-2019Q3] Simple Linux Utility for Resource Management
textproc/man2html [pkgsrc-2019Q3] Convert nroff(1) man pages to HTML
textproc/R-data.table [pkgsrc-2019Q3] Extension of data.frame
security/munge [pkgsrc-2019Q3] Authentication service for creating and validating credentials
biology/htslib [pkgsrc-2019Q3] C library for high-throughput sequencing data formats
archivers/libaec [pkgsrc-2019Q3] Adaptive entropy coding library
biology/trimmomatic [pkgsrc-2019Q3] Flexible read trimming tool for Illumina NGS data
textproc/R-cellranger [pkgsrc-2019Q3] Translate spreadsheet cell ranges to rows and columns
biology/bcftools [pkgsrc-2019Q3] Calling and manipulating files VCF and BCF formats
biology/plink [pkgsrc-2019Q3] Whole-genome association analysis toolset
biology/stacks [pkgsrc-2019Q3] Software pipeline for building loci from short-read sequences
biology/cdhit [pkgsrc-2019Q3] Clustering and comparing protein or nucleotide sequences
biology/kallisto [pkgsrc-2019Q3] Quantify abundances of transcripts from RNA-Seq data
biology/plinkseq [pkgsrc-2019Q3] C/C++ library for working with human genetic variation data
biology/vsearch [pkgsrc-2019Q3] Versatile open-source tool for metagenomics
biology/hisat2 [pkgsrc-2019Q3] Alignment program for mapping next-generation sequencing reads
devel/R-rematch [pkgsrc-2019Q3] Match regular expressions with a nicer API
devel/py-xopen [pkgsrc-2019Q3] Open compressed files transparently
devel/libctl [pkgsrc-2019Q3] Guile-based flexible control file library for scientific simulations
textproc/R-cellranger [pkgsrc-2019Q4] Translate spreadsheet cell ranges to rows and columns
math/arpack [pkgsrc-2019Q4] Library of subroutines to solve eigenvalue problems
biology/samtools [pkgsrc-2019Q4] Tools for manipulating next-generation sequencing data
biology/vsearch [pkgsrc-2019Q4] Versatile open-source tool for metagenomics
archivers/libaec [pkgsrc-2019Q4] Adaptive entropy coding library
devel/swig2 [pkgsrc-2019Q4] Simplified Wrapper and Interface Generator (version 2)
biology/stacks [pkgsrc-2019Q4] Software pipeline for building loci from short-read sequences
biology/ncbi-blast+ [pkgsrc-2019Q4] NCBI implementation of Basic Local Alignment Search Tool
textproc/man2html [pkgsrc-2019Q4] Convert nroff(1) man pages to HTML
devel/libctl [pkgsrc-2019Q4] Guile-based flexible control file library for scientific simulations
devel/py-xopen [pkgsrc-2019Q4] Open compressed files transparently
biology/hisat2 [pkgsrc-2019Q4] Alignment program for mapping next-generation sequencing reads
biology/bwa [pkgsrc-2019Q4] Map low-divergent sequences against a large reference genome
biology/fastp [pkgsrc-2019Q4] Ultra-fast all-in-one FASTQ preprocessor
biology/htslib [pkgsrc-2019Q4] C library for high-throughput sequencing data formats
biology/plink [pkgsrc-2019Q4] Whole-genome association analysis toolset
biology/canu [pkgsrc-2019Q4] Single molecule sequence assembler for genomes large and small
biology/bcftools [pkgsrc-2019Q4] Calling and manipulating files VCF and BCF formats
biology/plinkseq [pkgsrc-2019Q4] C/C++ library for working with human genetic variation data
parallel/slurm-wlm [pkgsrc-2019Q4] Simple Linux Utility for Resource Management
parallel/ganglia-monitor-core [pkgsrc-2019Q4] Ganglia cluster monitor, monitoring daemon
biology/trimmomatic [pkgsrc-2019Q4] Flexible read trimming tool for Illumina NGS data
biology/cdhit [pkgsrc-2019Q4] Clustering and comparing protein or nucleotide sequences
biology/kallisto [pkgsrc-2019Q4] Quantify abundances of transcripts from RNA-Seq data
textproc/R-data.table [pkgsrc-2019Q4] Extension of data.frame
devel/R-rematch [pkgsrc-2019Q4] Match regular expressions with a nicer API
security/munge [pkgsrc-2019Q4] Authentication service for creating and validating credentials
parallel/slurm-wlm [pkgsrc-2020Q1] Simple Linux Utility for Resource Management
devel/R-rematch [pkgsrc-2020Q1] Match regular expressions with a nicer API
biology/cdhit [pkgsrc-2020Q1] Clustering and comparing protein or nucleotide sequences
archivers/libaec [pkgsrc-2020Q1] Adaptive entropy coding library
biology/bcftools [pkgsrc-2020Q1] Calling and manipulating files VCF and BCF formats
biology/fastp [pkgsrc-2020Q1] Ultra-fast all-in-one FASTQ preprocessor
biology/trimmomatic [pkgsrc-2020Q1] Flexible read trimming tool for Illumina NGS data
devel/py-xopen [pkgsrc-2020Q1] Open compressed files transparently
devel/libctl [pkgsrc-2020Q1] Guile-based flexible control file library for scientific simulations
parallel/ganglia-monitor-core [pkgsrc-2020Q1] Ganglia cluster monitor, monitoring daemon
security/munge [pkgsrc-2020Q1] Authentication service for creating and validating credentials
biology/stacks [pkgsrc-2020Q1] Software pipeline for building loci from short-read sequences
devel/swig2 [pkgsrc-2020Q1] Simplified Wrapper and Interface Generator (version 2)
biology/samtools [pkgsrc-2020Q1] Tools for manipulating next-generation sequencing data
textproc/R-cellranger [pkgsrc-2020Q1] Translate spreadsheet cell ranges to rows and columns
textproc/R-data.table [pkgsrc-2020Q1] Extension of data.frame
biology/plinkseq [pkgsrc-2020Q1] C/C++ library for working with human genetic variation data
biology/kallisto [pkgsrc-2020Q1] Quantify abundances of transcripts from RNA-Seq data
biology/htslib [pkgsrc-2020Q1] C library for high-throughput sequencing data formats
biology/vsearch [pkgsrc-2020Q1] Versatile open-source tool for metagenomics
textproc/man2html [pkgsrc-2020Q1] Convert nroff(1) man pages to HTML
biology/ncbi-blast+ [pkgsrc-2020Q1] NCBI implementation of Basic Local Alignment Search Tool
biology/plink [pkgsrc-2020Q1] Whole-genome association analysis toolset
biology/bwa [pkgsrc-2020Q1] Map low-divergent sequences against a large reference genome
biology/canu [pkgsrc-2020Q1] Single molecule sequence assembler for genomes large and small
biology/hisat2 [pkgsrc-2020Q1] Alignment program for mapping next-generation sequencing reads
biology/vsearch [pkgsrc-2020Q2] Versatile open-source tool for metagenomics
biology/kallisto [pkgsrc-2020Q2] Quantify abundances of transcripts from RNA-Seq data
biology/ncbi-blast+ [pkgsrc-2020Q2] NCBI implementation of Basic Local Alignment Search Tool
textproc/man2html [pkgsrc-2020Q2] Convert nroff(1) man pages to HTML
security/munge [pkgsrc-2020Q2] Authentication service for creating and validating credentials
biology/canu [pkgsrc-2020Q2] Single molecule sequence assembler for genomes large and small
biology/bcftools [pkgsrc-2020Q2] Calling and manipulating files VCF and BCF formats
biology/hisat2 [pkgsrc-2020Q2] Alignment program for mapping next-generation sequencing reads
parallel/slurm-wlm [pkgsrc-2020Q2] Simple Linux Utility for Resource Management
textproc/R-data.table [pkgsrc-2020Q2] Extension of data.frame
biology/trimmomatic [pkgsrc-2020Q2] Flexible read trimming tool for Illumina NGS data
devel/libctl [pkgsrc-2020Q2] Guile-based flexible control file library for scientific simulations
devel/py-xopen [pkgsrc-2020Q2] Open compressed files transparently
devel/swig2 [pkgsrc-2020Q2] Simplified Wrapper and Interface Generator (version 2)
biology/htslib [pkgsrc-2020Q2] C library for high-throughput sequencing data formats
archivers/libaec [pkgsrc-2020Q2] Adaptive entropy coding library
parallel/ganglia-monitor-core [pkgsrc-2020Q2] Ganglia cluster monitor, monitoring daemon
devel/R-rematch [pkgsrc-2020Q2] Match regular expressions with a nicer API
biology/stacks [pkgsrc-2020Q2] Software pipeline for building loci from short-read sequences
biology/fastp [pkgsrc-2020Q2] Ultra-fast all-in-one FASTQ preprocessor
biology/bwa [pkgsrc-2020Q2] Map low-divergent sequences against a large reference genome
biology/plinkseq [pkgsrc-2020Q2] C/C++ library for working with human genetic variation data
textproc/R-cellranger [pkgsrc-2020Q2] Translate spreadsheet cell ranges to rows and columns
biology/samtools [pkgsrc-2020Q2] Tools for manipulating next-generation sequencing data
biology/plink [pkgsrc-2020Q2] Whole-genome association analysis toolset
biology/cdhit [pkgsrc-2020Q2] Clustering and comparing protein or nucleotide sequences
devel/libctl [pkgsrc-2020Q3] Guile-based flexible control file library for scientific simulations
biology/plinkseq [pkgsrc-2020Q3] C/C++ library for working with human genetic variation data
devel/R-rematch [pkgsrc-2020Q3] Match regular expressions with a nicer API
archivers/libaec [pkgsrc-2020Q3] Adaptive entropy coding library
parallel/slurm-wlm [pkgsrc-2020Q3] Simple Linux Utility for Resource Management
devel/swig2 [pkgsrc-2020Q3] Simplified Wrapper and Interface Generator (version 2)
textproc/R-data.table [pkgsrc-2020Q3] Extension of data.frame
biology/bcftools [pkgsrc-2020Q3] Tools for manipulating BCF and VCF variant call files
biology/plink [pkgsrc-2020Q3] Whole-genome association analysis toolset
biology/cdhit [pkgsrc-2020Q3] Clustering and comparing protein or nucleotide sequences
biology/bwa [pkgsrc-2020Q3] Map low-divergent sequences against a large reference genome
biology/stacks [pkgsrc-2020Q3] Software pipeline for building loci from short-read sequences
biology/htslib [pkgsrc-2020Q3] C library for high-throughput sequencing data formats
biology/fastp [pkgsrc-2020Q3] Ultra-fast all-in-one FASTQ preprocessor
biology/samtools [pkgsrc-2020Q3] Tools for manipulating sequence alignment maps
biology/kallisto [pkgsrc-2020Q3] Quantify abundances of transcripts from RNA-Seq data
biology/hisat2 [pkgsrc-2020Q3] Alignment program for mapping next-generation sequencing reads
biology/ncbi-blast+ [pkgsrc-2020Q3] NCBI implementation of Basic Local Alignment Search Tool
biology/vsearch [pkgsrc-2020Q3] Versatile open-source tool for metagenomics
textproc/man2html [pkgsrc-2020Q3] Convert nroff(1) man pages to HTML
textproc/R-cellranger [pkgsrc-2020Q3] Translate spreadsheet cell ranges to rows and columns
devel/py-xopen [pkgsrc-2020Q3] Open compressed files transparently
biology/trimmomatic [pkgsrc-2020Q3] Flexible read trimming tool for Illumina NGS data
biology/canu [pkgsrc-2020Q3] Single molecule sequence assembler for genomes large and small
security/munge [pkgsrc-2020Q3] Authentication service for creating and validating credentials
math/udunits [pkgsrc-2020Q3] Library and program for manipulating units of physical quantities
parallel/ganglia-monitor-core [pkgsrc-2020Q3] Ganglia cluster monitor, monitoring daemon
devel/libctl [pkgsrc-2020Q4] Guile-based flexible control file library for scientific simulations
textproc/R-cellranger [pkgsrc-2020Q4] Translate spreadsheet cell ranges to rows and columns
biology/cdhit [pkgsrc-2020Q4] Clustering and comparing protein or nucleotide sequences
biology/hisat2 [pkgsrc-2020Q4] Alignment program for mapping next-generation sequencing reads
textproc/R-data.table [pkgsrc-2020Q4] Extension of data.frame
devel/swig2 [pkgsrc-2020Q4] Simplified Wrapper and Interface Generator (version 2)
biology/vsearch [pkgsrc-2020Q4] Versatile open-source tool for metagenomics
biology/canu [pkgsrc-2020Q4] Single molecule sequence assembler for genomes large and small
biology/bcftools [pkgsrc-2020Q4] Tools for manipulating BCF and VCF variant call files
devel/py-xopen [pkgsrc-2020Q4] Open compressed files transparently
security/munge [pkgsrc-2020Q4] Authentication service for creating and validating credentials
biology/ncbi-blast+ [pkgsrc-2020Q4] NCBI implementation of Basic Local Alignment Search Tool
textproc/man2html [pkgsrc-2020Q4] Convert nroff(1) man pages to HTML
sysutils/auto-admin [pkgsrc-2020Q4] Portable tools for automating systems management
biology/stacks [pkgsrc-2020Q4] Software pipeline for building loci from short-read sequences
biology/fastp [pkgsrc-2020Q4] Ultra-fast all-in-one FASTQ preprocessor
biology/trimmomatic [pkgsrc-2020Q4] Flexible read trimming tool for Illumina NGS data
biology/htslib [pkgsrc-2020Q4] C library for high-throughput sequencing data formats
biology/kallisto [pkgsrc-2020Q4] Quantify abundances of transcripts from RNA-Seq data
biology/bwa [pkgsrc-2020Q4] Map low-divergent sequences against a large reference genome
parallel/ganglia-monitor-core [pkgsrc-2020Q4] Ganglia cluster monitor, monitoring daemon
devel/R-rematch [pkgsrc-2020Q4] Match regular expressions with a nicer API
math/udunits [pkgsrc-2020Q4] Library and program for manipulating units of physical quantities
biology/samtools [pkgsrc-2020Q4] Tools for manipulating sequence alignment maps
archivers/libaec [pkgsrc-2020Q4] Adaptive entropy coding library
biology/plink [pkgsrc-2020Q4] Whole-genome association analysis toolset
biology/plinkseq [pkgsrc-2020Q4] C/C++ library for working with human genetic variation data
parallel/slurm-wlm [pkgsrc-2020Q4] Simple Linux Utility for Resource Management
devel/py-xopen [pkgsrc-2021Q1] Open compressed files transparently
textproc/R-cellranger [pkgsrc-2021Q1] Translate spreadsheet cell ranges to rows and columns
devel/swig2 [pkgsrc-2021Q1] Simplified Wrapper and Interface Generator (version 2)
math/udunits [pkgsrc-2021Q1] Library and program for manipulating units of physical quantities
textproc/man2html [pkgsrc-2021Q1] Convert nroff(1) man pages to HTML
sysutils/auto-admin [pkgsrc-2021Q1] Portable tools for automating systems management
parallel/ganglia-monitor-core [pkgsrc-2021Q1] Ganglia cluster monitor, monitoring daemon
devel/R-rematch [pkgsrc-2021Q1] Match regular expressions with a nicer API
textproc/R-data.table [pkgsrc-2021Q1] Extension of data.frame
biology/generand [pkgsrc-2021Q1] Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
security/munge [pkgsrc-2021Q1] Authentication service for creating and validating credentials
biology/samtools [pkgsrc-2021Q1] Tools for manipulating sequence alignment maps
biology/vcf2hap [pkgsrc-2021Q1] Generate .hap file from VCF for haplohseq
biology/kallisto [pkgsrc-2021Q1] Quantify abundances of transcripts from RNA-Seq data
biology/vsearch [pkgsrc-2021Q1] Versatile open-source tool for metagenomics
biology/plink [pkgsrc-2021Q1] Whole-genome association analysis toolset
parallel/slurm-wlm [pkgsrc-2021Q1] Simple Linux Utility for Resource Management
biology/fastp [pkgsrc-2021Q1] Ultra-fast all-in-one FASTQ preprocessor
biology/bwa [pkgsrc-2021Q1] Map low-divergent sequences against a large reference genome
biology/plinkseq [pkgsrc-2021Q1] C/C++ library for working with human genetic variation data
biology/ncbi-blast+ [pkgsrc-2021Q1] NCBI implementation of Basic Local Alignment Search Tool
biology/trimmomatic [pkgsrc-2021Q1] Flexible read trimming tool for Illumina NGS data
biology/bowtie2 [pkgsrc-2021Q1] Ultrafast, memory-efficient short read aligner
biology/ad2vcf [pkgsrc-2021Q1] Add allelic depth info from a SAM stream to a VCF file
biology/py-dnaio [pkgsrc-2021Q1] Read and write FASTQ and FASTA files
archivers/libaec [pkgsrc-2021Q1] Adaptive entropy coding library
biology/bedtools [pkgsrc-2021Q1] Swiss army knife for genome arithmetic
biology/vcf-split [pkgsrc-2021Q1] Split a multi-sample VCF into single-sample VCFs
biology/cdhit [pkgsrc-2021Q1] Clustering and comparing protein or nucleotide sequences
biology/py-cutadapt [pkgsrc-2021Q1] Find and remove adapter sequences, primers, poly-A tails, etc
devel/libctl [pkgsrc-2021Q1] Guile-based flexible control file library for scientific simulations
biology/htslib [pkgsrc-2021Q1] C library for high-throughput sequencing data formats
biology/hisat2 [pkgsrc-2021Q1] Alignment program for mapping next-generation sequencing reads
biology/canu [pkgsrc-2021Q1] Single molecule sequence assembler for genomes large and small
biology/stacks [pkgsrc-2021Q1] Software pipeline for building loci from short-read sequences
biology/fastqc [pkgsrc-2021Q1] Quality control tool for high throughput sequence data
biology/bcftools [pkgsrc-2021Q1] Tools for manipulating BCF and VCF variant call files
biology/igv [pkgsrc-2021Q1] Visualization tool for genomic datasets
biology/biolibc [pkgsrc-2021Q1] Low-level high-performance bioinformatics library
devel/libctl [pkgsrc-2021Q2] Guile-based flexible control file library for scientific simulations
biology/generand [pkgsrc-2021Q2] Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
biology/ad2vcf [pkgsrc-2021Q2] Add allelic depth info from a SAM stream to a VCF file
biology/vcf-split [pkgsrc-2021Q2] Split a multi-sample VCF into single-sample VCFs
biology/bowtie2 [pkgsrc-2021Q2] Ultrafast, memory-efficient short read aligner
security/munge [pkgsrc-2021Q2] Authentication service for creating and validating credentials
biology/vcf2hap [pkgsrc-2021Q2] Generate .hap file from VCF for haplohseq
biology/trimmomatic [pkgsrc-2021Q2] Flexible read trimming tool for Illumina NGS data
biology/py-dnaio [pkgsrc-2021Q2] Read and write FASTQ and FASTA files
biology/plink [pkgsrc-2021Q2] Whole-genome association analysis toolset
biology/peak-classifier [pkgsrc-2021Q2] Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
biology/igv [pkgsrc-2021Q2] Visualization tool for genomic datasets
devel/py-xopen [pkgsrc-2021Q2] Open compressed files transparently
biology/fastqc [pkgsrc-2021Q2] Quality control tool for high throughput sequence data
math/udunits [pkgsrc-2021Q2] Library and program for manipulating units of physical quantities
biology/canu [pkgsrc-2021Q2] Single molecule sequence assembler for genomes large and small
biology/bwa [pkgsrc-2021Q2] Map low-divergent sequences against a large reference genome
biology/ncbi-blast+ [pkgsrc-2021Q2] NCBI implementation of Basic Local Alignment Search Tool
biology/py-cutadapt [pkgsrc-2021Q2] Find and remove adapter sequences, primers, poly-A tails, etc
devel/libxtend [pkgsrc-2021Q2] Miscellaneous functions to extend libc
biology/cdhit [pkgsrc-2021Q2] Clustering and comparing protein or nucleotide sequences
biology/samtools [pkgsrc-2021Q2] Tools for manipulating sequence alignment maps
biology/fastp [pkgsrc-2021Q2] Ultra-fast all-in-one FASTQ preprocessor
biology/kallisto [pkgsrc-2021Q2] Quantify abundances of transcripts from RNA-Seq data
biology/plinkseq [pkgsrc-2021Q2] C/C++ library for working with human genetic variation data
biology/htslib [pkgsrc-2021Q2] C library for high-throughput sequencing data formats
biology/bcftools [pkgsrc-2021Q2] Tools for manipulating BCF and VCF variant call files
biology/stacks [pkgsrc-2021Q2] Software pipeline for building loci from short-read sequences
biology/biolibc [pkgsrc-2021Q2] Low-level high-performance bioinformatics library
biology/bedtools [pkgsrc-2021Q2] Swiss army knife for genome arithmetic
biology/hisat2 [pkgsrc-2021Q2] Alignment program for mapping next-generation sequencing reads
archivers/libaec [pkgsrc-2021Q2] Adaptive entropy coding library
textproc/R-cellranger [pkgsrc-2021Q2] Translate spreadsheet cell ranges to rows and columns
devel/swig2 [pkgsrc-2021Q2] Simplified Wrapper and Interface Generator (version 2)
textproc/R-data.table [pkgsrc-2021Q2] Extension of data.frame
devel/R-rematch [pkgsrc-2021Q2] Match regular expressions with a nicer API
parallel/slurm-wlm [pkgsrc-2021Q2] Simple Linux Utility for Resource Management
biology/vsearch [pkgsrc-2021Q2] Versatile open-source tool for metagenomics
textproc/man2html [pkgsrc-2021Q2] Convert nroff(1) man pages to HTML
parallel/ganglia-monitor-core [pkgsrc-2021Q2] Ganglia cluster monitor, monitoring daemon
sysutils/auto-admin [pkgsrc-2021Q2] Portable tools for automating systems management
biology/trimmomatic [pkgsrc-2021Q3] Flexible read trimming tool for Illumina NGS data
devel/py-xopen [pkgsrc-2021Q3] Open compressed files transparently
biology/biolibc-tools [pkgsrc-2021Q3] High-performance bioinformatics tools based on biolibc
sysutils/auto-admin [pkgsrc-2021Q3] Portable tools for automating systems management
biology/vcf-split [pkgsrc-2021Q3] Split a multi-sample VCF into single-sample VCFs
biology/biolibc [pkgsrc-2021Q3] Low-level high-performance bioinformatics library
biology/cdhit [pkgsrc-2021Q3] Clustering and comparing protein or nucleotide sequences
biology/htslib [pkgsrc-2021Q3] C library for high-throughput sequencing data formats
biology/kallisto [pkgsrc-2021Q3] Quantify abundances of transcripts from RNA-Seq data
biology/ncbi-blast+ [pkgsrc-2021Q3] NCBI implementation of Basic Local Alignment Search Tool
biology/canu [pkgsrc-2021Q3] Single molecule sequence assembler for genomes large and small
biology/py-cutadapt [pkgsrc-2021Q3] Find and remove adapter sequences, primers, poly-A tails, etc
biology/generand [pkgsrc-2021Q3] Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
biology/samtools [pkgsrc-2021Q3] Tools for manipulating sequence alignment maps
biology/hisat2 [pkgsrc-2021Q3] Alignment program for mapping next-generation sequencing reads
biology/fastp [pkgsrc-2021Q3] Ultra-fast all-in-one FASTQ preprocessor
biology/stacks [pkgsrc-2021Q3] Software pipeline for building loci from short-read sequences
biology/py-dnaio [pkgsrc-2021Q3] Read and write FASTQ and FASTA files
biology/igv [pkgsrc-2021Q3] Visualization tool for genomic datasets
biology/bwa [pkgsrc-2021Q3] Map low-divergent sequences against a large reference genome
biology/bcftools [pkgsrc-2021Q3] Tools for manipulating BCF and VCF variant call files
biology/plink [pkgsrc-2021Q3] Whole-genome association analysis toolset
biology/bowtie2 [pkgsrc-2021Q3] Ultrafast, memory-efficient short read aligner
biology/plinkseq [pkgsrc-2021Q3] C/C++ library for working with human genetic variation data
archivers/libaec [pkgsrc-2021Q3] Adaptive entropy coding library
biology/peak-classifier [pkgsrc-2021Q3] Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
biology/bedtools [pkgsrc-2021Q3] Swiss army knife for genome arithmetic
biology/fastqc [pkgsrc-2021Q3] Quality control tool for high throughput sequence data
biology/vcf2hap [pkgsrc-2021Q3] Generate .hap file from VCF for haplohseq
biology/ad2vcf [pkgsrc-2021Q3] Add allelic depth info from a SAM stream to a VCF file
biology/vsearch [pkgsrc-2021Q3] Versatile open-source tool for metagenomics
devel/libxtend [pkgsrc-2021Q3] Miscellaneous functions to extend libc
biology/hisat2 [pkgsrc-2021Q4] Alignment program for mapping next-generation sequencing reads
biology/plinkseq [pkgsrc-2021Q4] C/C++ library for working with human genetic variation data
biology/generand [pkgsrc-2021Q4] Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
biology/plink [pkgsrc-2021Q4] Whole-genome association analysis toolset
biology/stacks [pkgsrc-2021Q4] Software pipeline for building loci from short-read sequences
devel/py-xopen [pkgsrc-2021Q4] Open compressed files transparently
devel/libxtend [pkgsrc-2021Q4] Miscellaneous functions to extend libc
biology/bedtools [pkgsrc-2021Q4] Swiss army knife for genome arithmetic
biology/vcf-split [pkgsrc-2021Q4] Split a multi-sample VCF into single-sample VCFs
biology/kallisto [pkgsrc-2021Q4] Quantify abundances of transcripts from RNA-Seq data
biology/biolibc [pkgsrc-2021Q4] Low-level high-performance bioinformatics library
biology/fastqc [pkgsrc-2021Q4] Quality control tool for high throughput sequence data
biology/htslib [pkgsrc-2021Q4] C library for high-throughput sequencing data formats
biology/py-cutadapt [pkgsrc-2021Q4] Find and remove adapter sequences, primers, poly-A tails, etc
biology/igv [pkgsrc-2021Q4] Visualization tool for genomic datasets
biology/fastp [pkgsrc-2021Q4] Ultra-fast all-in-one FASTQ preprocessor
biology/canu [pkgsrc-2021Q4] Single molecule sequence assembler for genomes large and small
biology/py-dnaio [pkgsrc-2021Q4] Read and write FASTQ and FASTA files
archivers/libaec [pkgsrc-2021Q4] Adaptive entropy coding library
sysutils/auto-admin [pkgsrc-2021Q4] Portable tools for automating systems management
biology/bowtie2 [pkgsrc-2021Q4] Ultrafast, memory-efficient short read aligner
biology/vcf2hap [pkgsrc-2021Q4] Generate .hap file from VCF for haplohseq
biology/peak-classifier [pkgsrc-2021Q4] Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
biology/samtools [pkgsrc-2021Q4] Tools for manipulating sequence alignment maps
biology/trimmomatic [pkgsrc-2021Q4] Flexible read trimming tool for Illumina NGS data
biology/biolibc-tools [pkgsrc-2021Q4] High-performance bioinformatics tools based on biolibc
biology/bwa [pkgsrc-2021Q4] Map low-divergent sequences against a large reference genome
biology/ad2vcf [pkgsrc-2021Q4] Add allelic depth info from a SAM stream to a VCF file
biology/ncbi-blast+ [pkgsrc-2021Q4] NCBI implementation of Basic Local Alignment Search Tool
biology/cdhit [pkgsrc-2021Q4] Clustering and comparing protein or nucleotide sequences
biology/bcftools [pkgsrc-2021Q4] Tools for manipulating BCF and VCF variant call files
biology/vsearch [pkgsrc-2021Q4] Versatile open-source tool for metagenomics
biology/samtools [pkgsrc-2022Q1] Tools for manipulating sequence alignment maps
biology/kallisto [pkgsrc-2022Q1] Quantify abundances of transcripts from RNA-Seq data
biology/py-cutadapt [pkgsrc-2022Q1] Find and remove adapter sequences, primers, poly-A tails, etc
biology/bowtie2 [pkgsrc-2022Q1] Ultrafast, memory-efficient short read aligner
biology/py-dnaio [pkgsrc-2022Q1] Read and write FASTQ and FASTA files
biology/cdhit [pkgsrc-2022Q1] Clustering and comparing protein or nucleotide sequences
sysutils/auto-admin [pkgsrc-2022Q1] Portable tools for automating systems management
biology/stacks [pkgsrc-2022Q1] Software pipeline for building loci from short-read sequences
biology/vcf2hap [pkgsrc-2022Q1] Generate .hap file from VCF for haplohseq
biology/biolibc [pkgsrc-2022Q1] Low-level high-performance bioinformatics library
biology/ad2vcf [pkgsrc-2022Q1] Add allelic depth info from a SAM stream to a VCF file
biology/bwa [pkgsrc-2022Q1] Map low-divergent sequences against a large reference genome
biology/vsearch [pkgsrc-2022Q1] Versatile open-source tool for metagenomics
biology/bedtools [pkgsrc-2022Q1] Swiss army knife for genome arithmetic
biology/plink [pkgsrc-2022Q1] Whole-genome association analysis toolset
biology/biolibc-tools [pkgsrc-2022Q1] High-performance bioinformatics tools based on biolibc
biology/fastp [pkgsrc-2022Q1] Ultra-fast all-in-one FASTQ preprocessor
biology/plinkseq [pkgsrc-2022Q1] C/C++ library for working with human genetic variation data
biology/hisat2 [pkgsrc-2022Q1] Alignment program for mapping next-generation sequencing reads
biology/canu [pkgsrc-2022Q1] Single molecule sequence assembler for genomes large and small
biology/igv [pkgsrc-2022Q1] Visualization tool for genomic datasets
biology/vcf-split [pkgsrc-2022Q1] Split a multi-sample VCF into single-sample VCFs
archivers/libaec [pkgsrc-2022Q1] Adaptive entropy coding library
devel/libxtend [pkgsrc-2022Q1] Miscellaneous functions to extend libc
devel/py-xopen [pkgsrc-2022Q1] Open compressed files transparently
biology/trimmomatic [pkgsrc-2022Q1] Flexible read trimming tool for Illumina NGS data
biology/generand [pkgsrc-2022Q1] Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
biology/ncbi-blast+ [pkgsrc-2022Q1] NCBI implementation of Basic Local Alignment Search Tool
biology/bcftools [pkgsrc-2022Q1] Tools for manipulating BCF and VCF variant call files
biology/htslib [pkgsrc-2022Q1] C library for high-throughput sequencing data formats
biology/fastqc [pkgsrc-2022Q1] Quality control tool for high throughput sequence data
biology/peak-classifier [pkgsrc-2022Q1] Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
biology/plinkseq [pkgsrc-2022Q2] C/C++ library for working with human genetic variation data
devel/libgtextutils [pkgsrc-2022Q2] Gordon text utilities
biology/kallisto [pkgsrc-2022Q2] Quantify abundances of transcripts from RNA-Seq data
biology/biolibc-tools [pkgsrc-2022Q2] High-performance bioinformatics tools based on biolibc
biology/py-cutadapt [pkgsrc-2022Q2] Find and remove adapter sequences, primers, poly-A tails, etc
biology/vcf-split [pkgsrc-2022Q2] Split a multi-sample VCF into single-sample VCFs
biology/plink [pkgsrc-2022Q2] Whole-genome association analysis toolset
math/basic-stats [pkgsrc-2022Q2] Command-line tool to perform basic statistics on tabular data
devel/simde [pkgsrc-2022Q2] Header-only library for SIMD intrinsics
biology/bowtie2 [pkgsrc-2022Q2] Ultrafast, memory-efficient short read aligner
biology/htslib [pkgsrc-2022Q2] C library for high-throughput sequencing data formats
biology/peak-classifier [pkgsrc-2022Q2] Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
biology/ncbi-blast+ [pkgsrc-2022Q2] NCBI implementation of Basic Local Alignment Search Tool
biology/canu [pkgsrc-2022Q2] Single molecule sequence assembler for genomes large and small
biology/vcf2hap [pkgsrc-2022Q2] Generate .hap file from VCF for haplohseq
biology/generand [pkgsrc-2022Q2] Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
biology/cdhit [pkgsrc-2022Q2] Clustering and comparing protein or nucleotide sequences
biology/hisat2 [pkgsrc-2022Q2] Alignment program for mapping next-generation sequencing reads
biology/igv [pkgsrc-2022Q2] Visualization tool for genomic datasets
biology/fastx-toolkit [pkgsrc-2022Q2] CLI tools for Short-Reads FASTA/FASTQ files preprocessing
biology/bedtools [pkgsrc-2022Q2] Swiss army knife for genome arithmetic
biology/fastp [pkgsrc-2022Q2] Ultra-fast all-in-one FASTQ preprocessor
devel/libxtend [pkgsrc-2022Q2] Miscellaneous functions to extend libc
biology/bwa [pkgsrc-2022Q2] Map low-divergent sequences against a large reference genome
archivers/libaec [pkgsrc-2022Q2] Adaptive entropy coding library
sysutils/auto-admin [pkgsrc-2022Q2] Portable tools for automating systems management
biology/trimmomatic [pkgsrc-2022Q2] Flexible read trimming tool for Illumina NGS data
biology/vsearch [pkgsrc-2022Q2] Versatile open-source tool for metagenomics
biology/samtools [pkgsrc-2022Q2] Tools for manipulating sequence alignment maps
biology/ad2vcf [pkgsrc-2022Q2] Add allelic depth info from a SAM stream to a VCF file
biology/py-dnaio [pkgsrc-2022Q2] Read and write FASTQ and FASTA files
biology/stacks [pkgsrc-2022Q2] Software pipeline for building loci from short-read sequences
biology/bcftools [pkgsrc-2022Q2] Tools for manipulating BCF and VCF variant call files
biology/biolibc [pkgsrc-2022Q2] Low-level high-performance bioinformatics library
biology/fastqc [pkgsrc-2022Q2] Quality control tool for high throughput sequence data
devel/py-xopen [pkgsrc-2022Q2] Open compressed files transparently
archivers/libaec [pkgsrc-2022Q3] Adaptive entropy coding library
biology/bedtools [pkgsrc-2022Q3] Swiss army knife for genome arithmetic
biology/igv [pkgsrc-2022Q3] Visualization tool for genomic datasets
math/basic-stats [pkgsrc-2022Q3] Command-line tool to perform basic statistics on tabular data
biology/py-cutadapt [pkgsrc-2022Q3] Find and remove adapter sequences, primers, poly-A tails, etc
biology/bwa [pkgsrc-2022Q3] Map low-divergent sequences against a large reference genome
biology/htslib [pkgsrc-2022Q3] C library for high-throughput sequencing data formats
biology/plinkseq [pkgsrc-2022Q3] C/C++ library for working with human genetic variation data
biology/peak-classifier [pkgsrc-2022Q3] Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
biology/ad2vcf [pkgsrc-2022Q3] Add allelic depth info from a SAM stream to a VCF file
biology/vcf-split [pkgsrc-2022Q3] Split a multi-sample VCF into single-sample VCFs
biology/canu [pkgsrc-2022Q3] Single molecule sequence assembler for genomes large and small
biology/bowtie2 [pkgsrc-2022Q3] Ultrafast, memory-efficient short read aligner
biology/py-dnaio [pkgsrc-2022Q3] Read and write FASTQ and FASTA files
biology/kallisto [pkgsrc-2022Q3] Quantify abundances of transcripts from RNA-Seq data
biology/fastqc [pkgsrc-2022Q3] Quality control tool for high throughput sequence data
biology/bcftools [pkgsrc-2022Q3] Tools for manipulating BCF and VCF variant call files
biology/cdhit [pkgsrc-2022Q3] Clustering and comparing protein or nucleotide sequences
sysutils/auto-admin [pkgsrc-2022Q3] Portable tools for automating systems management
devel/py-xopen [pkgsrc-2022Q3] Open compressed files transparently
devel/simde [pkgsrc-2022Q3] Header-only library for SIMD intrinsics
devel/libgtextutils [pkgsrc-2022Q3] Gordon text utilities
biology/stacks [pkgsrc-2022Q3] Software pipeline for building loci from short-read sequences
biology/fastp [pkgsrc-2022Q3] Ultra-fast all-in-one FASTQ preprocessor
biology/generand [pkgsrc-2022Q3] Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
biology/ncbi-blast+ [pkgsrc-2022Q3] NCBI implementation of Basic Local Alignment Search Tool
biology/hisat2 [pkgsrc-2022Q3] Alignment program for mapping next-generation sequencing reads
biology/plink [pkgsrc-2022Q3] Whole-genome association analysis toolset
biology/vsearch [pkgsrc-2022Q3] Versatile open-source tool for metagenomics
biology/samtools [pkgsrc-2022Q3] Tools for manipulating sequence alignment maps
biology/trimmomatic [pkgsrc-2022Q3] Flexible read trimming tool for Illumina NGS data
biology/vcf2hap [pkgsrc-2022Q3] Generate .hap file from VCF for haplohseq
biology/biolibc [pkgsrc-2022Q3] Low-level high-performance bioinformatics library
biology/biolibc-tools [pkgsrc-2022Q3] High-performance bioinformatics tools based on biolibc
biology/fastx-toolkit [pkgsrc-2022Q3] CLI tools for Short-Reads FASTA/FASTQ files preprocessing
devel/libxtend [pkgsrc-2022Q3] Miscellaneous functions to extend libc
biology/ncbi-blast+ [pkgsrc-2022Q4] NCBI implementation of Basic Local Alignment Search Tool
biology/hisat2 [pkgsrc-2022Q4] Alignment program for mapping next-generation sequencing reads
biology/bedtools [pkgsrc-2022Q4] Swiss army knife for genome arithmetic
biology/plink [pkgsrc-2022Q4] Whole-genome association analysis toolset
biology/peak-classifier [pkgsrc-2022Q4] Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
biology/igv [pkgsrc-2022Q4] Visualization tool for genomic datasets
biology/vsearch [pkgsrc-2022Q4] Versatile open-source tool for metagenomics
biology/gffread [pkgsrc-2022Q4] GFF/GTF format conversions, filtering, FASTA extraction, etc
biology/bcftools [pkgsrc-2022Q4] Tools for manipulating BCF and VCF variant call files
biology/rna-seq [pkgsrc-2022Q4] Core tools needed for RNA-Seq analysis
math/basic-stats [pkgsrc-2022Q4] Command-line tool to perform basic statistics on tabular data
devel/simde [pkgsrc-2022Q4] Header-only library for SIMD intrinsics
biology/vcf2hap [pkgsrc-2022Q4] Generate .hap file from VCF for haplohseq
biology/samtools [pkgsrc-2022Q4] Tools for manipulating sequence alignment maps
biology/bwa [pkgsrc-2022Q4] Map low-divergent sequences against a large reference genome
biology/ad2vcf [pkgsrc-2022Q4] Add allelic depth info from a SAM stream to a VCF file
biology/canu [pkgsrc-2022Q4] Single molecule sequence assembler for genomes large and small
biology/py-cutadapt [pkgsrc-2022Q4] Find and remove adapter sequences, primers, poly-A tails, etc
biology/fastq-trim [pkgsrc-2022Q4] Lightening fast sequence read trimmer
biology/kallisto [pkgsrc-2022Q4] Quantify abundances of transcripts from RNA-Seq data
biology/py-dnaio [pkgsrc-2022Q4] Read and write FASTQ and FASTA files
biology/generand [pkgsrc-2022Q4] Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
biology/bowtie2 [pkgsrc-2022Q4] Ultrafast, memory-efficient short read aligner
biology/cdhit [pkgsrc-2022Q4] Clustering and comparing protein or nucleotide sequences
biology/biolibc-tools [pkgsrc-2022Q4] High-performance bioinformatics tools based on biolibc
biology/trimmomatic [pkgsrc-2022Q4] Flexible read trimming tool for Illumina NGS data
biology/fasda [pkgsrc-2022Q4] Fast and simple differential analysis
biology/vcf-split [pkgsrc-2022Q4] Split a multi-sample VCF into single-sample VCFs
biology/biolibc [pkgsrc-2022Q4] Low-level high-performance bioinformatics library
biology/fastp [pkgsrc-2022Q4] Ultra-fast all-in-one FASTQ preprocessor
biology/fastx-toolkit [pkgsrc-2022Q4] CLI tools for Short-Reads FASTA/FASTQ files preprocessing
biology/htslib [pkgsrc-2022Q4] C library for high-throughput sequencing data formats
archivers/libaec [pkgsrc-2022Q4] Adaptive entropy coding library
sysutils/auto-admin [pkgsrc-2022Q4] Portable tools for automating systems management
devel/libgtextutils [pkgsrc-2022Q4] Gordon text utilities
biology/plinkseq [pkgsrc-2022Q4] C/C++ library for working with human genetic variation data
devel/libxtend [pkgsrc-2022Q4] Miscellaneous functions to extend libc
biology/fastqc [pkgsrc-2022Q4] Quality control tool for high throughput sequence data
devel/py-xopen [pkgsrc-2022Q4] Open compressed files transparently
biology/stacks [pkgsrc-2022Q4] Software pipeline for building loci from short-read sequences