The following packages were found for maintainer: bacon@NetBSD.org
wip/py-graph-tool [CURRENT] Python module for manipulation and statistical analysis of graphs
wip/gromacs2018 [CURRENT] Molecular dynamics package
wip/munge [CURRENT] Authentication service for creating and validating credentials
wip/trinity [CURRENT] Assembles transcript sequences from Illumina RNA-Seq data
biology/trimmomatic [CURRENT] Flexible read trimming tool for Illumina NGS data
wip/rainbow [CURRENT] Short reads clustering and local assembly
biology/samtools [CURRENT] Tools for manipulating sequence alignment maps
wip/twintk [CURRENT] Terminal Windows Toolkit
wip/epacts [CURRENT] Efficient and Parallelizable Association Container Toolbox
wip/ufc [CURRENT] Unified framework for finite element assembly
wip/suitesparse [CURRENT] SuiteSparse is a set of packages for sparse matrices calculation
biology/bowtie2 [CURRENT] Ultrafast, memory-efficient short read aligner
wip/libaec [CURRENT] Adaptive entropy coding library
wip/mst-bench [CURRENT] Maximum sustainable throughput benchmark
wip/salmon [CURRENT] Transcript-level quantification of RNA-seq from lightweight alignments
wip/seqtk [CURRENT] Tool for processing sequences in FASTA/FASTQ format
wip/metal [CURRENT] Meta-analysis of genomewide association scans
wip/vcf-split [CURRENT] Split a multi-sample VCF into single-sample VCFs
wip/pbcopper [CURRENT] Core C++ library for data structures, algorithms, and utilities
wip/ape [CURRENT] Another Programmers Editor
wip/basic-stats [CURRENT] Command-line tool to perform basic statistics on tabular data
wip/cdhit [CURRENT] Clustering and comparing protein or nucleotide sequences
wip/dazz_db [CURRENT] Dresden assembler for long read DNA projects
wip/fasttree [CURRENT] Approximately-maximum-likelihood phylogenetic trees from alignments
wip/canu [CURRENT] Single molecule sequence assembler for genomes large and small
wip/ad2vcf [CURRENT] Add allelic depth info from a SAM stream to a VCF file
wip/jellyfish2 [CURRENT] Fast, memory-efficient counting of k-mers in DNA
wip/ganglia-webfrontend [CURRENT] PHP based frontend for the Ganglia Cluster Monitor
wip/bowtie2 [CURRENT] Ultrafast, memory-efficient short read aligner
wip/tbb [CURRENT] Library that provides thread building blocks
wip/fvcom2 [CURRENT] Prognostic coastal ocean circulation model
wip/slurm-wlm-devel [CURRENT] Simple Linux Utility for Resource Management
wip/man2html [CURRENT] Convert nroff(1) man pages to HTML
wip/p5-IPC-Open3-Simple [CURRENT] Simple alternative to IPC::Open3
wip/py-ffc [CURRENT] C++ code generator for multilinear forms
wip/cdbfasta [CURRENT] Fast indexing and retrieval of fasta records from flat file databases
devel/py-xopen [CURRENT] Open compressed files transparently
wip/py-pypeflow [CURRENT] Lightweight and reusable make/flow data process library
wip/cut-and-run [CURRENT] Split a text file into segments and process in parallel
wip/smithwaterman [CURRENT] Smith-waterman-gotoh alignment algorithm
wip/p5-transdecoder [CURRENT] Identify candidate coding regions within transcript sequences
wip/bwa [CURRENT] Map low-divergent sequences against a large reference genome
wip/pear [CURRENT] Memory-efficient and highly accurate pair-end read merger
wip/pkg-dev [CURRENT] Scripts to automate common tasks in pkgsrc development
wip/bedtools [CURRENT] Swiss army knife for genome arithmetic
wip/plink2 [CURRENT] Whole genome association analysis toolset
wip/prodigal [CURRENT] Prokaryotic Dynamic Programming Genefinding Algorithm
biology/bedtools [CURRENT] Swiss army knife for genome arithmetic
wip/pooler [CURRENT] Optimise DNA sequencing primer-set combinations
wip/plink [CURRENT] Whole genome association analysis toolset
wip/py-anvio [CURRENT] Analysis and visualization platform for omics data
wip/numactl [CURRENT] Non Uniform Memory Access tools
wip/libxtend [CURRENT] Miscellaneous functions to extend libc
wip/igv [CURRENT] Visualization tool for genomic datasets
wip/py-biopython [CURRENT] Collection of Python modules for bioinformatics
biology/ad2vcf [CURRENT] Add allelic depth info from a SAM stream to a VCF file
biology/ncbi-blast+ [CURRENT] NCBI implementation of Basic Local Alignment Search Tool
wip/libzeep [CURRENT] Make it easy to create SOAP servers
wip/tabixpp [CURRENT] C++ wrapper to tabix indexer
wip/ncbi-blast+ [CURRENT] NCBI implementation of Basic Local Alignment Search Tool
biology/htslib [CURRENT] C library for high-throughput sequencing data formats
wip/fastool [CURRENT] Simple and quick FastQ and FastA tool for file reading and conversion
biology/py-dnaio [CURRENT] Read and write FASTQ and FASTA files
wip/libbacon [CURRENT] Miscellaneous experimental functions
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/singularity [CURRENT] Application container for Linux
wip/vcftools [CURRENT] Tools for working with VCF genomics files
wip/haplohseq [CURRENT] Identify regions of allelic imbalance
wip/ddocent [CURRENT] Bash pipeline for RAD sequencing
wip/mpb [CURRENT] MIT Photonic Bands
biology/igv [CURRENT] Visualization tool for genomic datasets
wip/daligner [CURRENT] Find all significant local alignments between reads
wip/dlpoly-classic [CURRENT] General purpose classical molecular dynamics
wip/runas [CURRENT] Wrapper around su for running a command as another user
wip/rsem [CURRENT] RNA-Seq by Expectation-Maximization
wip/htslib [CURRENT] C library for high-throughput sequencing data formats
wip/cluster-admin [CURRENT] HPC cluster admin tools
biology/plinkseq [CURRENT] C/C++ library for working with human genetic variation data
biology/plink [CURRENT] Whole-genome association analysis toolset
wip/bolt-lmm [CURRENT] Statistics for testing association between phenotype and genotypes
wip/vcf2hap [CURRENT] Generate .hap file from VCF for haplohseq
wip/p5-trimgalore [CURRENT] Wrapper around Cutadapt and FastQC for adapter and quality trimming
biology/bwa [CURRENT] Map low-divergent sequences against a large reference genome
wip/denyhosts [CURRENT] Block hosts with too many failed login attempts
wip/vcflib [CURRENT] C++ library and CLI tools for parsing and manipulating VCF files
biology/cdhit [CURRENT] Clustering and comparing protein or nucleotide sequences
wip/jellyfish [CURRENT] Fast, memory-efficient counting of k-mers in DNA
wip/gmap [CURRENT] Genomic Mapping and Alignment Program for mRNA and EST Sequences
wip/py-pbfalcon [CURRENT] Experimental PacBio diploid assembler
wip/linux-ukbgene [CURRENT] Tool for accessing UK Biobank data
wip/blasr_libcpp [CURRENT] Library for analyzing PacBio sequences
wip/lmod [CURRENT] Dynamic modification of a users environment
wip/detab [CURRENT] Replace tabs with spaces in a text file
wip/hisat2 [CURRENT] Alignment program for mapping next-generation sequencing reads
wip/blasr [CURRENT] PacBio(R) long read aligner
biology/generand [CURRENT] Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
wip/xssp [CURRENT] Software for creating DSSP and HSSP files
wip/py-pysam [CURRENT] Python module for reading, manipulating and writing genomic data sets
wip/R-optparse [CURRENT] Command Line Option Parser
wip/famsa [CURRENT] Algorithm for large-scale multiple sequence alignments
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/py-htseq [CURRENT] Framework to analyze data from high-throughput sequencing assays
wip/meep [CURRENT] FDTD simulation software to model electromagnetic systems
wip/antlr [CURRENT] ANother Tool for Language Recognition
wip/fastaunique [CURRENT] Sort and uniq fasta files
wip/webbrowser [CURRENT] Proxy script for launching best available web browser
wip/wgrib2 [CURRENT] Tools for managing GRIB weather data files
wip/py-ufl [CURRENT] Unified Form Language for finite element discretizations
wip/wip-tools [CURRENT] Tools for developing wip packages
wip/bowtie [CURRENT] Ultrafast, memory-efficient short read aligner
wip/unanimity [CURRENT] Consensus library and applications
wip/biolibc [CURRENT] Low-level high-performance bioinformatics library
wip/bcftools [CURRENT] Tools for manipulating BCF and VCF variant call files
wip/filevercmp [CURRENT] Filevercmp function as in sort --version-sort
wip/udunits2 [CURRENT] Library for manipulating units of physical quantities
wip/fftw-openmpi [CURRENT] Collection of fast C routines to compute DFTs
sysutils/auto-admin [CURRENT] Portable tools for automating systems management
wip/fbsd2pkg [CURRENT] Convert a FreeBSD port framework to a pkgsrc package
wip/fastx-toolkit [CURRENT] CLI tools for Short-Reads FASTA/FASTQ files preprocessing
wip/fsom [CURRENT] Tiny C library for managing SOM (Self-Organizing Maps) neural networks
wip/slclust [CURRENT] Single-linkage clustering with Jaccard similarity
biology/hisat2 [CURRENT] Alignment program for mapping next-generation sequencing reads
wip/bpcscripts [CURRENT] Gast Illumina processing
archivers/libaec [CURRENT] Adaptive entropy coding library
wip/py-rdfextras [CURRENT] Collection of packages providing extras based on RDFLib 3
wip/R-getopt [CURRENT] C-Like getopt Behavior
wip/kallisto [CURRENT] Quantify abundances of transcripts from RNA-Seq data
wip/structure [CURRENT] Multi-locus genotype data to investigate population structure
wip/R-mpfr [CURRENT] Multiple Precision Floating Point Arithmetic for R
biology/peak-classifier [CURRENT] Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
wip/mcl [CURRENT] Fast and scalable unsupervised cluster algorithm for graphs
wip/armadillo [CURRENT] C++ linear algebra library
wip/gromacs [CURRENT] Molecular dynamics package
wip/cereal [CURRENT] C++11 library for serialization
wip/mpb-openmpi [CURRENT] MIT Photonic Bands
wip/centrifuge [CURRENT] Novel microbial classification engine
wip/hmmer [CURRENT] Profile hidden Markov models for biological sequence analysis
wip/multichoose [CURRENT] Generate multiset combinations (n multichoose k)
wip/py-fiat [CURRENT] Finite element Automatic Tabulator
biology/kallisto [CURRENT] Quantify abundances of transcripts from RNA-Seq data
wip/muscle [CURRENT] MUltiple Sequence Comparison by Log-Expectation
devel/libxtend [CURRENT] Miscellaneous functions to extend libc
wip/spcm [CURRENT] Simple, portable cluster management
biology/bcftools [CURRENT] Tools for manipulating BCF and VCF variant call files
biology/canu [CURRENT] Single molecule sequence assembler for genomes large and small
wip/fastp [CURRENT] Ultra-fast all-in-one FASTQ preprocessor
biology/vsearch [CURRENT] Versatile open-source tool for metagenomics
wip/pbbam [CURRENT] PacBio BAM C++ library, with SWIG bindings
wip/openmpi [CURRENT] Open source implementation
wip/vsearch [CURRENT] Versatile open-source tool for metagenomics
biology/py-cutadapt [CURRENT] Find and remove adapter sequences, primers, poly-A tails, etc
wip/py-snakemake [CURRENT] Reduce the complexity of creating workflows
wip/peak-classifier [CURRENT] Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
wip/subread [CURRENT] High-performance read alignment, quantification and mutation discovery
wip/py-macs2 [CURRENT] Novel algorithm for identifying transcript factor binding sites
wip/tophat [CURRENT] Fast splice junction mapper for RNA-Seq reads
wip/py-rdflib340 [CURRENT] Python library for RDF manipulation
wip/libpare [CURRENT] Pointer Array Regular Expressions
wip/gemma [CURRENT] Genome-wide Efficient Mixed Model Association
wip/openmx-openmpi [CURRENT] Nano-scale material simulations based on DFT
wip/yaggo [CURRENT] Generate command line parser using getopt_long
wip/py-viper [CURRENT] Scientific plotter and run-time visualization module
wip/generand [CURRENT] Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
biology/vcf-split [CURRENT] Split a multi-sample VCF into single-sample VCFs
biology/stacks [CURRENT] Software pipeline for building loci from short-read sequences
biology/fastp [CURRENT] Ultra-fast all-in-one FASTQ preprocessor
wip/samtools [CURRENT] Tools for manipulating sequence alignment maps
wip/intervaltree [CURRENT] Minimal C++ interval tree implementation
wip/docviewer [CURRENT] Generic command to automatically select a document viewer
biology/biolibc [CURRENT] Low-level high-performance bioinformatics library
wip/auto-admin [CURRENT] Portable tools for automating systems management
wip/meep-openmpi [CURRENT] FDTD simulation software to model electromagnetic systems
biology/vcf2hap [CURRENT] Generate .hap file from VCF for haplohseq
wip/linux-gcta [CURRENT] Tool for Genome-wide Complex Trait Analysis
wip/fftw-mpich [CURRENT] Collection of fast C routines to compute DFTs
wip/slurm-wlm [CURRENT] Simple Linux Utility for Resource Management
wip/packmol [CURRENT] Pack molecules in defined regions of space
wip/gtextutils [CURRENT] Gordon text utilities
wip/pbseqan [CURRENT] PacBio patched and stripped down seqan
wip/meep-mpi [CURRENT] FDTD simulation software to model electromagnetic systems
wip/py-hostlist [CURRENT] Manage SLURM host lists
biology/fastqc [CURRENT] Quality control tool for high throughput sequence data
devel/py-xopen [pkgsrc-2017Q4] Open compressed files transparently
biology/bwa [pkgsrc-2017Q4] Map low-divergent sequences against a large reference genome
security/munge [pkgsrc-2018Q1] Authentication service for creating and validating credentials
biology/bwa [pkgsrc-2018Q1] Map low-divergent sequences against a large reference genome
textproc/man2html [pkgsrc-2018Q1] Convert nroff(1) man pages to HTML
parallel/slurm [pkgsrc-2018Q1] Simple Linux Utility for Resource Management
devel/py-xopen [pkgsrc-2018Q1] Open compressed files transparently
security/munge [pkgsrc-2018Q2] Authentication service for creating and validating credentials
biology/samtools [pkgsrc-2018Q2] Tools for manipulating next-generation sequencing data
biology/bwa [pkgsrc-2018Q2] Map low-divergent sequences against a large reference genome
biology/htslib [pkgsrc-2018Q2] C library for high-throughput sequencing data formats
devel/py-xopen [pkgsrc-2018Q2] Open compressed files transparently
parallel/slurm-wlm [pkgsrc-2018Q2] Simple Linux Utility for Resource Management
parallel/ganglia-monitor-core [pkgsrc-2018Q2] Ganglia cluster monitor, monitoring daemon
biology/ncbi-blast+ [pkgsrc-2018Q2] NCBI implementation of Basic Local Alignment Search Tool
textproc/man2html [pkgsrc-2018Q2] Convert nroff(1) man pages to HTML
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
biology/ncbi-blast+ [pkgsrc-2018Q3] NCBI implementation of Basic Local Alignment Search Tool
parallel/slurm-wlm [pkgsrc-2018Q3] Simple Linux Utility for Resource Management
devel/py-xopen [pkgsrc-2018Q3] Open compressed files transparently
parallel/ganglia-monitor-core [pkgsrc-2018Q3] Ganglia cluster monitor, monitoring daemon
security/munge [pkgsrc-2018Q3] Authentication service for creating and validating credentials
biology/bwa [pkgsrc-2018Q3] Map low-divergent sequences against a large reference genome
textproc/man2html [pkgsrc-2018Q3] Convert nroff(1) man pages to HTML
parallel/ganglia-monitor-core [pkgsrc-2018Q4] Ganglia cluster monitor, monitoring daemon
parallel/slurm-wlm [pkgsrc-2018Q4] Simple Linux Utility for Resource Management
biology/trimmomatic [pkgsrc-2018Q4] Flexible read trimming tool for Illumina NGS data
biology/stacks [pkgsrc-2018Q4] Software pipeline for building loci from short-read sequences
biology/bwa [pkgsrc-2018Q4] Map low-divergent sequences against a large reference genome
biology/kallisto [pkgsrc-2018Q4] Quantify abundances of transcripts from RNA-Seq data
biology/samtools [pkgsrc-2018Q4] Tools for manipulating next-generation sequencing data
biology/htslib [pkgsrc-2018Q4] C library for high-throughput sequencing data formats
biology/ncbi-blast+ [pkgsrc-2018Q4] NCBI implementation of Basic Local Alignment Search Tool
security/munge [pkgsrc-2018Q4] Authentication service for creating and validating credentials
devel/py-xopen [pkgsrc-2018Q4] Open compressed files transparently
textproc/man2html [pkgsrc-2018Q4] Convert nroff(1) man pages to HTML
parallel/ganglia-monitor-core [pkgsrc-2019Q1] Ganglia cluster monitor, monitoring daemon
textproc/man2html [pkgsrc-2019Q1] Convert nroff(1) man pages to HTML
biology/cdhit [pkgsrc-2019Q1] Clustering and comparing protein or nucleotide sequences
biology/hisat2 [pkgsrc-2019Q1] Alignment program for mapping next-generation sequencing reads
biology/kallisto [pkgsrc-2019Q1] Quantify abundances of transcripts from RNA-Seq data
biology/trimmomatic [pkgsrc-2019Q1] Flexible read trimming tool for Illumina NGS data
biology/stacks [pkgsrc-2019Q1] Software pipeline for building loci from short-read sequences
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/plinkseq [pkgsrc-2019Q1] C/C++ library for working with human genetic variation data
biology/samtools [pkgsrc-2019Q1] Tools for manipulating next-generation sequencing data
biology/htslib [pkgsrc-2019Q1] C library for high-throughput sequencing data formats
biology/ncbi-blast+ [pkgsrc-2019Q1] NCBI implementation of Basic Local Alignment Search Tool
biology/bcftools [pkgsrc-2019Q1] Calling and manipulating files VCF and BCF formats
devel/swig2 [pkgsrc-2019Q1] Simplified Wrapper and Interface Generator (version 2)
security/munge [pkgsrc-2019Q1] Authentication service for creating and validating credentials
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
devel/libctl [pkgsrc-2019Q1] Guile-based flexible control file library for scientific simulations
biology/plinkseq [pkgsrc-2019Q2] C/C++ library for working with human genetic variation data
biology/trimmomatic [pkgsrc-2019Q2] Flexible read trimming tool for Illumina NGS data
biology/fastp [pkgsrc-2019Q2] Ultra-fast all-in-one FASTQ preprocessor
biology/bwa [pkgsrc-2019Q2] Map low-divergent sequences against a large reference genome
biology/plink [pkgsrc-2019Q2] Whole-genome association analysis toolset
devel/libctl [pkgsrc-2019Q2] Guile-based flexible control file library for scientific simulations
biology/cdhit [pkgsrc-2019Q2] Clustering and comparing protein or nucleotide sequences
biology/hisat2 [pkgsrc-2019Q2] Alignment program for mapping next-generation sequencing reads
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
biology/ncbi-blast+ [pkgsrc-2019Q2] NCBI implementation of Basic Local Alignment Search Tool
devel/swig2 [pkgsrc-2019Q2] Simplified Wrapper and Interface Generator (version 2)
security/munge [pkgsrc-2019Q2] Authentication service for creating and validating credentials
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
parallel/ganglia-monitor-core [pkgsrc-2019Q2] Ganglia cluster monitor, monitoring daemon
math/arpack [pkgsrc-2019Q2] Library of subroutines to solve eigenvalue problems
biology/vsearch [pkgsrc-2019Q2] Versatile open-source tool for metagenomics
devel/py-xopen [pkgsrc-2019Q2] Open compressed files transparently
biology/stacks [pkgsrc-2019Q2] Software pipeline for building loci from short-read sequences
parallel/slurm-wlm [pkgsrc-2019Q2] Simple Linux Utility for Resource Management
textproc/man2html [pkgsrc-2019Q2] Convert nroff(1) man pages to HTML
biology/htslib [pkgsrc-2019Q2] C library for high-throughput sequencing data formats
biology/ncbi-blast+ [pkgsrc-2019Q3] NCBI implementation of Basic Local Alignment Search Tool
math/arpack [pkgsrc-2019Q3] Library of subroutines to solve eigenvalue problems
parallel/ganglia-monitor-core [pkgsrc-2019Q3] Ganglia cluster monitor, monitoring daemon
devel/R-rematch [pkgsrc-2019Q3] Match regular expressions with a nicer API
biology/fastp [pkgsrc-2019Q3] Ultra-fast all-in-one FASTQ preprocessor
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/samtools [pkgsrc-2019Q3] Tools for manipulating next-generation sequencing data
parallel/slurm-wlm [pkgsrc-2019Q3] Simple Linux Utility for Resource Management
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/bwa [pkgsrc-2019Q3] Map low-divergent sequences against a large reference genome
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
biology/canu [pkgsrc-2019Q3] Single molecule sequence assembler for genomes large and small
devel/py-xopen [pkgsrc-2019Q3] Open compressed files transparently
devel/libctl [pkgsrc-2019Q3] Guile-based flexible control file library for scientific simulations
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
devel/swig2 [pkgsrc-2019Q3] Simplified Wrapper and Interface Generator (version 2)
biology/fastp [pkgsrc-2019Q4] Ultra-fast all-in-one FASTQ preprocessor
biology/plinkseq [pkgsrc-2019Q4] C/C++ library for working with human genetic variation data
biology/ncbi-blast+ [pkgsrc-2019Q4] NCBI implementation of Basic Local Alignment Search Tool
security/munge [pkgsrc-2019Q4] Authentication service for creating and validating credentials
devel/R-rematch [pkgsrc-2019Q4] Match regular expressions with a nicer API
parallel/ganglia-monitor-core [pkgsrc-2019Q4] Ganglia cluster monitor, monitoring daemon
parallel/slurm-wlm [pkgsrc-2019Q4] Simple Linux Utility for Resource Management
math/arpack [pkgsrc-2019Q4] Library of subroutines to solve eigenvalue problems
biology/kallisto [pkgsrc-2019Q4] Quantify abundances of transcripts from RNA-Seq data
biology/cdhit [pkgsrc-2019Q4] Clustering and comparing protein or nucleotide sequences
biology/trimmomatic [pkgsrc-2019Q4] Flexible read trimming tool for Illumina NGS data
biology/bcftools [pkgsrc-2019Q4] Calling and manipulating files VCF and BCF formats
biology/canu [pkgsrc-2019Q4] Single molecule sequence assembler for genomes large and small
biology/plink [pkgsrc-2019Q4] Whole-genome association analysis toolset
textproc/R-cellranger [pkgsrc-2019Q4] Translate spreadsheet cell ranges to rows and columns
textproc/R-data.table [pkgsrc-2019Q4] Extension of data.frame
devel/py-xopen [pkgsrc-2019Q4] Open compressed files transparently
devel/libctl [pkgsrc-2019Q4] Guile-based flexible control file library for scientific simulations
archivers/libaec [pkgsrc-2019Q4] Adaptive entropy coding library
biology/vsearch [pkgsrc-2019Q4] Versatile open-source tool for metagenomics
biology/samtools [pkgsrc-2019Q4] Tools for manipulating next-generation sequencing data
biology/htslib [pkgsrc-2019Q4] C library for high-throughput sequencing data formats
devel/swig2 [pkgsrc-2019Q4] Simplified Wrapper and Interface Generator (version 2)
biology/stacks [pkgsrc-2019Q4] Software pipeline for building loci from short-read sequences
textproc/man2html [pkgsrc-2019Q4] Convert nroff(1) man pages to HTML
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/trimmomatic [pkgsrc-2020Q1] Flexible read trimming tool for Illumina NGS data
biology/kallisto [pkgsrc-2020Q1] Quantify abundances of transcripts from RNA-Seq data
biology/plinkseq [pkgsrc-2020Q1] C/C++ library for working with human genetic variation data
textproc/man2html [pkgsrc-2020Q1] Convert nroff(1) man pages to HTML
biology/htslib [pkgsrc-2020Q1] C library for high-throughput sequencing data formats
biology/vsearch [pkgsrc-2020Q1] Versatile open-source tool for metagenomics
biology/stacks [pkgsrc-2020Q1] Software pipeline for building loci from short-read sequences
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
devel/swig2 [pkgsrc-2020Q1] Simplified Wrapper and Interface Generator (version 2)
textproc/R-data.table [pkgsrc-2020Q1] Extension of data.frame
parallel/ganglia-monitor-core [pkgsrc-2020Q1] Ganglia cluster monitor, monitoring daemon
devel/libctl [pkgsrc-2020Q1] Guile-based flexible control file library for scientific simulations
parallel/slurm-wlm [pkgsrc-2020Q1] Simple Linux Utility for Resource Management
textproc/R-cellranger [pkgsrc-2020Q1] Translate spreadsheet cell ranges to rows and columns
devel/py-xopen [pkgsrc-2020Q1] Open compressed files transparently
biology/samtools [pkgsrc-2020Q1] Tools for manipulating next-generation sequencing data
security/munge [pkgsrc-2020Q1] Authentication service for creating and validating credentials
devel/R-rematch [pkgsrc-2020Q1] Match regular expressions with a nicer API
biology/fastp [pkgsrc-2020Q1] Ultra-fast all-in-one FASTQ preprocessor
biology/hisat2 [pkgsrc-2020Q1] Alignment program for mapping next-generation sequencing reads
archivers/libaec [pkgsrc-2020Q1] Adaptive entropy coding library
biology/cdhit [pkgsrc-2020Q1] Clustering and comparing protein or nucleotide sequences
biology/bcftools [pkgsrc-2020Q1] Calling and manipulating files VCF and BCF formats
biology/plink [pkgsrc-2020Q2] Whole-genome association analysis toolset
textproc/R-cellranger [pkgsrc-2020Q2] Translate spreadsheet cell ranges to rows and columns
biology/bwa [pkgsrc-2020Q2] Map low-divergent sequences against a large reference genome
archivers/libaec [pkgsrc-2020Q2] Adaptive entropy coding library
parallel/ganglia-monitor-core [pkgsrc-2020Q2] Ganglia cluster monitor, monitoring daemon
parallel/slurm-wlm [pkgsrc-2020Q2] Simple Linux Utility for Resource Management
biology/htslib [pkgsrc-2020Q2] C library for high-throughput sequencing data formats
biology/hisat2 [pkgsrc-2020Q2] Alignment program for mapping next-generation sequencing reads
biology/trimmomatic [pkgsrc-2020Q2] Flexible read trimming tool for Illumina NGS data
biology/kallisto [pkgsrc-2020Q2] Quantify abundances of transcripts from RNA-Seq data
devel/swig2 [pkgsrc-2020Q2] Simplified Wrapper and Interface Generator (version 2)
textproc/R-data.table [pkgsrc-2020Q2] Extension of data.frame
security/munge [pkgsrc-2020Q2] Authentication service for creating and validating credentials
textproc/man2html [pkgsrc-2020Q2] Convert nroff(1) man pages to HTML
biology/ncbi-blast+ [pkgsrc-2020Q2] NCBI implementation of Basic Local Alignment Search Tool
devel/libctl [pkgsrc-2020Q2] Guile-based flexible control file library for scientific simulations
devel/py-xopen [pkgsrc-2020Q2] Open compressed files transparently
biology/bcftools [pkgsrc-2020Q2] Calling and manipulating files VCF and BCF formats
biology/canu [pkgsrc-2020Q2] Single molecule sequence assembler for genomes large and small
biology/cdhit [pkgsrc-2020Q2] Clustering and comparing protein or nucleotide sequences
biology/vsearch [pkgsrc-2020Q2] Versatile open-source tool for metagenomics
biology/samtools [pkgsrc-2020Q2] Tools for manipulating next-generation sequencing data
biology/plinkseq [pkgsrc-2020Q2] C/C++ library for working with human genetic variation data
biology/fastp [pkgsrc-2020Q2] Ultra-fast all-in-one FASTQ preprocessor
biology/stacks [pkgsrc-2020Q2] Software pipeline for building loci from short-read sequences
devel/R-rematch [pkgsrc-2020Q2] Match regular expressions with a nicer API
parallel/slurm-wlm [pkgsrc-2020Q3] Simple Linux Utility for Resource Management
biology/stacks [pkgsrc-2020Q3] Software pipeline for building loci from short-read sequences
devel/libctl [pkgsrc-2020Q3] Guile-based flexible control file library for scientific simulations
math/udunits [pkgsrc-2020Q3] Library and program for manipulating units of physical quantities
devel/swig2 [pkgsrc-2020Q3] Simplified Wrapper and Interface Generator (version 2)
archivers/libaec [pkgsrc-2020Q3] Adaptive entropy coding library
devel/R-rematch [pkgsrc-2020Q3] Match regular expressions with a nicer API
parallel/ganglia-monitor-core [pkgsrc-2020Q3] Ganglia cluster monitor, monitoring daemon
security/munge [pkgsrc-2020Q3] Authentication service for creating and validating credentials
biology/canu [pkgsrc-2020Q3] Single molecule sequence assembler for genomes large and small
textproc/R-data.table [pkgsrc-2020Q3] Extension of data.frame
biology/trimmomatic [pkgsrc-2020Q3] Flexible read trimming tool for Illumina NGS data
devel/py-xopen [pkgsrc-2020Q3] Open compressed files transparently
textproc/R-cellranger [pkgsrc-2020Q3] Translate spreadsheet cell ranges to rows and columns
textproc/man2html [pkgsrc-2020Q3] Convert nroff(1) man pages to HTML
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/vsearch [pkgsrc-2020Q3] Versatile open-source tool for metagenomics
biology/ncbi-blast+ [pkgsrc-2020Q3] NCBI implementation of Basic Local Alignment Search Tool
biology/hisat2 [pkgsrc-2020Q3] Alignment program for mapping next-generation sequencing reads
biology/kallisto [pkgsrc-2020Q3] Quantify abundances of transcripts from RNA-Seq data
biology/samtools [pkgsrc-2020Q3] Tools for manipulating sequence alignment maps
biology/fastp [pkgsrc-2020Q3] Ultra-fast all-in-one FASTQ preprocessor
biology/htslib [pkgsrc-2020Q3] C library for high-throughput sequencing data formats
biology/plinkseq [pkgsrc-2020Q3] C/C++ library for working with human genetic variation data
math/udunits [pkgsrc-2020Q4] Library and program for manipulating units of physical quantities
textproc/man2html [pkgsrc-2020Q4] Convert nroff(1) man pages to HTML
biology/bcftools [pkgsrc-2020Q4] Tools for manipulating BCF and VCF variant call files
parallel/slurm-wlm [pkgsrc-2020Q4] Simple Linux Utility for Resource Management
sysutils/auto-admin [pkgsrc-2020Q4] Portable tools for automating systems management
biology/ncbi-blast+ [pkgsrc-2020Q4] NCBI implementation of Basic Local Alignment Search Tool
biology/stacks [pkgsrc-2020Q4] Software pipeline for building loci from short-read sequences
biology/kallisto [pkgsrc-2020Q4] Quantify abundances of transcripts from RNA-Seq data
biology/plinkseq [pkgsrc-2020Q4] C/C++ library for working with human genetic variation data
biology/fastp [pkgsrc-2020Q4] Ultra-fast all-in-one FASTQ preprocessor
biology/cdhit [pkgsrc-2020Q4] Clustering and comparing protein or nucleotide sequences
biology/samtools [pkgsrc-2020Q4] Tools for manipulating sequence alignment maps
security/munge [pkgsrc-2020Q4] Authentication service for creating and validating credentials
devel/swig2 [pkgsrc-2020Q4] Simplified Wrapper and Interface Generator (version 2)
devel/libctl [pkgsrc-2020Q4] Guile-based flexible control file library for scientific simulations
biology/hisat2 [pkgsrc-2020Q4] Alignment program for mapping next-generation sequencing reads
textproc/R-cellranger [pkgsrc-2020Q4] Translate spreadsheet cell ranges to rows and columns
archivers/libaec [pkgsrc-2020Q4] Adaptive entropy coding library
parallel/ganglia-monitor-core [pkgsrc-2020Q4] Ganglia cluster monitor, monitoring daemon
biology/bwa [pkgsrc-2020Q4] Map low-divergent sequences against a large reference genome
biology/htslib [pkgsrc-2020Q4] C library for high-throughput sequencing data formats
biology/plink [pkgsrc-2020Q4] Whole-genome association analysis toolset
biology/canu [pkgsrc-2020Q4] Single molecule sequence assembler for genomes large and small
biology/trimmomatic [pkgsrc-2020Q4] Flexible read trimming tool for Illumina NGS data
biology/vsearch [pkgsrc-2020Q4] Versatile open-source tool for metagenomics
textproc/R-data.table [pkgsrc-2020Q4] Extension of data.frame
devel/py-xopen [pkgsrc-2020Q4] Open compressed files transparently
devel/R-rematch [pkgsrc-2020Q4] Match regular expressions with a nicer API
biology/biolibc [pkgsrc-2021Q1] Low-level high-performance bioinformatics library
biology/py-dnaio [pkgsrc-2021Q1] Read and write FASTQ and FASTA files
biology/vcf2hap [pkgsrc-2021Q1] Generate .hap file from VCF for haplohseq
sysutils/auto-admin [pkgsrc-2021Q1] Portable tools for automating systems management
textproc/R-cellranger [pkgsrc-2021Q1] Translate spreadsheet cell ranges to rows and columns
parallel/ganglia-monitor-core [pkgsrc-2021Q1] Ganglia cluster monitor, monitoring daemon
biology/py-cutadapt [pkgsrc-2021Q1] Find and remove adapter sequences, primers, poly-A tails, etc
biology/ad2vcf [pkgsrc-2021Q1] Add allelic depth info from a SAM stream to a VCF file
devel/libctl [pkgsrc-2021Q1] Guile-based flexible control file library for scientific simulations
devel/R-rematch [pkgsrc-2021Q1] Match regular expressions with a nicer API
archivers/libaec [pkgsrc-2021Q1] Adaptive entropy coding library
biology/bedtools [pkgsrc-2021Q1] Swiss army knife for genome arithmetic
biology/bowtie2 [pkgsrc-2021Q1] Ultrafast, memory-efficient short read aligner
textproc/man2html [pkgsrc-2021Q1] Convert nroff(1) man pages to HTML
biology/vsearch [pkgsrc-2021Q1] Versatile open-source tool for metagenomics
biology/htslib [pkgsrc-2021Q1] C library for high-throughput sequencing data formats
devel/swig2 [pkgsrc-2021Q1] Simplified Wrapper and Interface Generator (version 2)
biology/plink [pkgsrc-2021Q1] Whole-genome association analysis toolset
biology/hisat2 [pkgsrc-2021Q1] Alignment program for mapping next-generation sequencing reads
parallel/slurm-wlm [pkgsrc-2021Q1] Simple Linux Utility for Resource Management
biology/fastp [pkgsrc-2021Q1] Ultra-fast all-in-one FASTQ preprocessor
devel/py-xopen [pkgsrc-2021Q1] Open compressed files transparently
biology/bwa [pkgsrc-2021Q1] Map low-divergent sequences against a large reference genome
biology/canu [pkgsrc-2021Q1] Single molecule sequence assembler for genomes large and small
biology/plinkseq [pkgsrc-2021Q1] C/C++ library for working with human genetic variation data
biology/kallisto [pkgsrc-2021Q1] Quantify abundances of transcripts from RNA-Seq data
security/munge [pkgsrc-2021Q1] Authentication service for creating and validating credentials
biology/ncbi-blast+ [pkgsrc-2021Q1] NCBI implementation of Basic Local Alignment Search Tool
biology/samtools [pkgsrc-2021Q1] Tools for manipulating sequence alignment maps
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/vcf-split [pkgsrc-2021Q1] Split a multi-sample VCF into single-sample VCFs
math/udunits [pkgsrc-2021Q1] Library and program for manipulating units of physical quantities
biology/generand [pkgsrc-2021Q1] Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
textproc/R-data.table [pkgsrc-2021Q1] Extension of data.frame
biology/cdhit [pkgsrc-2021Q1] Clustering and comparing protein or nucleotide sequences
biology/igv [pkgsrc-2021Q1] Visualization tool for genomic datasets
biology/trimmomatic [pkgsrc-2021Q1] Flexible read trimming tool for Illumina NGS data
textproc/R-cellranger [pkgsrc-2021Q2] Translate spreadsheet cell ranges to rows and columns
archivers/libaec [pkgsrc-2021Q2] Adaptive entropy coding library
biology/hisat2 [pkgsrc-2021Q2] Alignment program for mapping next-generation sequencing reads
biology/kallisto [pkgsrc-2021Q2] Quantify abundances of transcripts from RNA-Seq data
biology/bedtools [pkgsrc-2021Q2] Swiss army knife for genome arithmetic
biology/biolibc [pkgsrc-2021Q2] Low-level high-performance bioinformatics library
biology/stacks [pkgsrc-2021Q2] Software pipeline for building loci from short-read sequences
biology/bcftools [pkgsrc-2021Q2] Tools for manipulating BCF and VCF variant call files
devel/libctl [pkgsrc-2021Q2] Guile-based flexible control file library for scientific simulations
biology/htslib [pkgsrc-2021Q2] C library for high-throughput sequencing data formats
devel/R-rematch [pkgsrc-2021Q2] Match regular expressions with a nicer API
biology/igv [pkgsrc-2021Q2] Visualization tool for genomic datasets
biology/peak-classifier [pkgsrc-2021Q2] Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
biology/plink [pkgsrc-2021Q2] Whole-genome association analysis toolset
biology/py-dnaio [pkgsrc-2021Q2] Read and write FASTQ and FASTA files
biology/trimmomatic [pkgsrc-2021Q2] Flexible read trimming tool for Illumina NGS data
biology/vcf2hap [pkgsrc-2021Q2] Generate .hap file from VCF for haplohseq
biology/bowtie2 [pkgsrc-2021Q2] Ultrafast, memory-efficient short read aligner
biology/vcf-split [pkgsrc-2021Q2] Split a multi-sample VCF into single-sample VCFs
biology/ad2vcf [pkgsrc-2021Q2] Add allelic depth info from a SAM stream to a VCF file
biology/samtools [pkgsrc-2021Q2] Tools for manipulating sequence alignment maps
biology/generand [pkgsrc-2021Q2] Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
biology/vsearch [pkgsrc-2021Q2] Versatile open-source tool for metagenomics
devel/libxtend [pkgsrc-2021Q2] Miscellaneous functions to extend libc
devel/py-xopen [pkgsrc-2021Q2] Open compressed files transparently
security/munge [pkgsrc-2021Q2] Authentication service for creating and validating credentials
biology/plinkseq [pkgsrc-2021Q2] C/C++ library for working with human genetic variation data
textproc/R-data.table [pkgsrc-2021Q2] Extension of data.frame
parallel/ganglia-monitor-core [pkgsrc-2021Q2] Ganglia cluster monitor, monitoring daemon
parallel/slurm-wlm [pkgsrc-2021Q2] Simple Linux Utility for Resource Management
devel/swig2 [pkgsrc-2021Q2] Simplified Wrapper and Interface Generator (version 2)
textproc/man2html [pkgsrc-2021Q2] Convert nroff(1) man pages to HTML
sysutils/auto-admin [pkgsrc-2021Q2] Portable tools for automating systems management
biology/fastp [pkgsrc-2021Q2] Ultra-fast all-in-one FASTQ preprocessor
biology/cdhit [pkgsrc-2021Q2] Clustering and comparing protein or nucleotide sequences
biology/py-cutadapt [pkgsrc-2021Q2] Find and remove adapter sequences, primers, poly-A tails, etc
biology/ncbi-blast+ [pkgsrc-2021Q2] NCBI implementation of Basic Local Alignment Search Tool
biology/bwa [pkgsrc-2021Q2] Map low-divergent sequences against a large reference genome
biology/canu [pkgsrc-2021Q2] Single molecule sequence assembler for genomes large and small
math/udunits [pkgsrc-2021Q2] Library and program for manipulating units of physical quantities
biology/fastqc [pkgsrc-2021Q2] Quality control tool for high throughput sequence data