The following packages were found for maintainer: bacon@netbsd.org
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wip/bwa Map low-divergent sequences against a large reference genome
biology/trimmomatic Flexible read trimming tool for Illumina NGS data
wip/meep-openmpi FDTD simulation software to model electromagnetic systems
wip/fastahack Utilities for indexing and sequence extraction from FASTA files
wip/stacks Software pipeline for building loci from short-read sequences
wip/parafly Process the commands in parallel on a single server
wip/vcftools Tools for working with VCF genomics files
wip/ddocent Bash pipeline for RAD sequencing
wip/mpb MIT Photonic Bands
wip/daligner Find all significant local alignments between reads
wip/rsem RNA-Seq by Expectation-Maximization
wip/htslib C library for high-throughput sequencing data formats
wip/cluster-admin HPC cluster admin tools
wip/bolt-lmm Statistics for testing association between phenotype and genotypes
wip/p5-trimgalore Wrapper around Cutadapt and FastQC for adapter and quality trimming
biology/bwa Map low-divergent sequences against a large reference genome
wip/denyhosts Block hosts with too many failed login attempts
wip/vcflib C++ library and CLI tools for parsing and manipulating VCF files
biology/cdhit Clustering and comparing protein or nucleotide sequences
wip/ape Another Programmers Editor
wip/auto-dev Tools for automating code development and documentation
wip/dlpoly-classic General purpose classical molecular dynamics
wip/gmap Genomic Mapping and Alignment Program for mRNA and EST Sequences
wip/py-pbfalcon Experimental PacBio diploid assembler
wip/linux-ukbgene Tool for accessing UK Biobank data
wip/lmod Dynamic modification of a users environment
wip/blasr PacBio(R) long read aligner
biology/plink Whole-genome association analysis toolset
biology/plinkseq C/C++ library for working with human genetic variation data
wip/py-pysam Python module for reading, manipulating and writing genomic data sets
wip/R-optparse Command Line Option Parser
wip/famsa Algorithm for large-scale multiple sequence alignments
wip/py-ete3 Python Environment for (phylogenetic) Tree Exploration
wip/py-eggnog-mapper Fast functional annotation of novel DNA or protein sequences
wip/py-htseq Framework to analyze data from high-throughput sequencing assays
wip/antlr ANother Tool for Language Recognition
wip/fsom Tiny C library for managing SOM (Self-Organizing Maps) neural networks
biology/hisat2 Alignment program for mapping next-generation sequencing reads
wip/bpcscripts Gast Illumina processing
wip/structure Multi-locus genotype data to investigate population structure
wip/R-mpfr Multiple Precision Floating Point Arithmetic for R
devel/libxtend Miscellaneous functions to extend libc
wip/mcl Fast and scalable unsupervised cluster algorithm for graphs
wip/cereal C++11 library for serialization
wip/mpb-openmpi MIT Photonic Bands
wip/multichoose Generate multiset combinations (n multichoose k)
biology/kallisto Quantify abundances of transcripts from RNA-Seq data
wip/muscle MUltiple Sequence Comparison by Log-Expectation
biology/bcftools Tools for manipulating BCF and VCF variant call files
biology/vsearch Versatile open-source tool for metagenomics
wip/py-macs2 Novel algorithm for identifying transcript factor binding sites
biology/stacks Software pipeline for building loci from short-read sequences
wip/samtools Tools for manipulating sequence alignment maps
biology/vcf2hap Generate .hap file from VCF for haplohseq
wip/linux-gcta Tool for Genome-wide Complex Trait Analysis
wip/slurm-wlm Simple Linux Utility for Resource Management
wip/packmol Pack molecules in defined regions of space
wip/py-hostlist Manage SLURM host lists
wip/prodigal Prokaryotic Dynamic Programming Genefinding Algorithm
wip/igv Visualization tool for genomic datasets
wip/munge Authentication service for creating and validating credentials
wip/trinity Assembles transcript sequences from Illumina RNA-Seq data
wip/seqtk Tool for processing sequences in FASTA/FASTQ format
wip/vcf-split Split a multi-sample VCF into single-sample VCFs
wip/metal Meta-analysis of genomewide association scans
wip/rainbow Short reads clustering and local assembly
biology/py-dnaio Read and write FASTQ and FASTA files
wip/cut-and-run Split a text file into segments and process in parallel
wip/man2html Convert nroff(1) man pages to HTML
biology/biolibc Low-level high-performance bioinformatics library
wip/docviewer Generic command to automatically select a document viewer
wip/generand Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
wip/openmx-openmpi Nano-scale material simulations based on DFT
wip/gemma Genome-wide Efficient Mixed Model Association
wip/R-getopt C-Like getopt Behavior
wip/vcf2hap Generate .hap file from VCF for haplohseq
wip/fastaunique Sort and uniq fasta files
wip/webbrowser Proxy script for launching best available web browser
wip/wgrib2 Tools for managing GRIB weather data files
wip/py-ufl Unified Form Language for finite element discretizations
wip/bowtie Ultrafast, memory-efficient short read aligner
wip/biolibc Low-level high-performance bioinformatics library
sysutils/auto-admin Portable tools for automating systems management
wip/cdhit Clustering and comparing protein or nucleotide sequences
biology/generand Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
wip/singularity Application container for Linux
wip/haplohseq Identify regions of allelic imbalance
biology/igv Visualization tool for genomic datasets
wip/jellyfish Fast, memory-efficient counting of k-mers in DNA
biology/peak-classifier Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
wip/armadillo C++ linear algebra library
wip/py-snakemake Reduce the complexity of creating workflows
wip/tophat Fast splice junction mapper for RNA-Seq reads
wip/py-viper Scientific plotter and run-time visualization module
biology/fastqc Quality control tool for high throughput sequence data
wip/bowtie2 Ultrafast, memory-efficient short read aligner
wip/slurm-wlm-devel Simple Linux Utility for Resource Management
wip/p5-IPC-Open3-Simple Simple alternative to IPC::Open3
wip/pkg-dev Scripts to automate common tasks in pkgsrc development
wip/plink2 Whole genome association analysis toolset
wip/pooler Optimise DNA sequencing primer-set combinations
wip/plink Whole genome association analysis toolset
wip/numactl Non Uniform Memory Access tools
wip/libxtend Miscellaneous functions to extend libc
biology/ad2vcf Add allelic depth info from a SAM stream to a VCF file
biology/ncbi-blast+ NCBI implementation of Basic Local Alignment Search Tool
wip/ncbi-blast+ NCBI implementation of Basic Local Alignment Search Tool
wip/basic-stats Command-line tool to perform basic statistics on tabular data
wip/libaec Adaptive entropy coding library
biology/bowtie2 Ultrafast, memory-efficient short read aligner
wip/epacts Efficient and Parallelizable Association Container Toolbox
biology/bedtools Swiss army knife for genome arithmetic
wip/bedtools Swiss army knife for genome arithmetic
biology/vcf-split Split a multi-sample VCF into single-sample VCFs
wip/udunits2 Library for manipulating units of physical quantities
wip/blasr_libcpp Library for analyzing PacBio sequences
wip/slclust Single-linkage clustering with Jaccard similarity
archivers/libaec Adaptive entropy coding library
wip/meep FDTD simulation software to model electromagnetic systems
wip/py-ffc C++ code generator for multilinear forms
biology/biolibc-tools High-performance bioinformatics tools based on biolibc
biology/py-cutadapt Find and remove adapter sequences, primers, poly-A tails, etc
wip/tabixpp C++ wrapper to tabix indexer
wip/gromacs2018 Molecular dynamics package
wip/fastool Simple and quick FastQ and FastA tool for file reading and conversion
biology/htslib C library for high-throughput sequencing data formats
wip/ad2vcf Add allelic depth info from a SAM stream to a VCF file
wip/centrifuge Novel microbial classification engine
wip/auto-admin Portable tools for automating systems management
wip/detab Replace tabs with spaces in a text file
wip/biolibc-tools High-performance bioinformatics tools based on biolibc
wip/smithwaterman Smith-waterman-gotoh alignment algorithm
wip/canu Single molecule sequence assembler for genomes large and small
wip/meep-mpi FDTD simulation software to model electromagnetic systems
biology/fastp Ultra-fast all-in-one FASTQ preprocessor
wip/libpare Pointer Array Regular Expressions
biology/canu Single molecule sequence assembler for genomes large and small
biology/samtools Tools for manipulating sequence alignment maps
wip/fastq-trim Lightening fast sequence read trimmer
wip/py-bcbio-gff Read and write Generic Feature Format (GFF) with Biopython integration
wip/py-dna-features-viewer Python library to visualize DNA features, e.g. GenBank or Gff files
wip/python3 Wrapper linking current python3.x to python3 and python
wip/globalprotect-openconnect OpenConnect GUI for GlobalProtect protocol
wip/microsynteny-tools Tools for exploring microsyntenic differences among species
wip/subread High-performance read alignment, quantification and mutation discovery
wip/hisat2 Alignment program for mapping next-generation sequencing reads
wip/hisat2-simde Alignment program for mapping next-generation sequencing reads
wip/py-graph-tool Python module for manipulation and statistical analysis of graphs
wip/pear Memory-efficient and highly accurate pair-end read merger
wip/fastp Ultra-fast all-in-one FASTQ preprocessor
wip/fasttree Approximately-maximum-likelihood phylogenetic trees from alignments
wip/jellyfish2 Fast, memory-efficient counting of k-mers in DNA
wip/kallisto Quantify abundances of transcripts from RNA-Seq data
wip/salmon Transcript-level quantification of RNA-seq from lightweight alignments
wip/spcm Simple, portable cluster management
wip/cdbfasta Fast indexing and retrieval of fasta records from flat file databases
wip/wip-tools Tools for developing wip packages
wip/intervaltree Minimal C++ interval tree implementation
wip/py-rdfextras Collection of packages providing extras based on RDFLib 3
wip/dazz_db Dresden assembler for long read DNA projects
wip/yaggo Generate command line parser using getopt_long
wip/ufc Unified framework for finite element assembly
wip/mst-bench Maximum sustainable throughput benchmark
wip/py-rdflib340 Python library for RDF manipulation
wip/vsearch Versatile open-source tool for metagenomics
wip/filevercmp Filevercmp function as in sort --version-sort
wip/bcftools Tools for manipulating BCF and VCF variant call files
wip/lpjs Lightweight, Portable Job Scheduler
wip/twintk Terminal Windows Toolkit
devel/py-xopen Open compressed files transparently
wip/p5-transdecoder Identify candidate coding regions within transcript sequences
wip/py-pypeflow Lightweight and reusable make/flow data process library
wip/fbsd2pkg Convert a FreeBSD port framework to a pkgsrc package
wip/gromacs Molecular dynamics package
wip/py-fiat Finite element Automatic Tabulator
wip/xssp Software for creating DSSP and HSSP files
wip/hmmer Profile hidden Markov models for biological sequence analysis
wip/fftw-openmpi Collection of fast C routines to compute DFTs
wip/fastx-toolkit CLI tools for Short-Reads FASTA/FASTQ files preprocessing
wip/py-anvio Analysis and visualization platform for omics data
wip/libzeep Make it easy to create SOAP servers
wip/peak-classifier Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
wip/runas Wrapper around su for running a command as another user
devel/simde Header-only library for SIMD intrinsics
wip/libgtextutils Gordon text utilities
devel/libgtextutils Gordon text utilities
biology/fastx-toolkit CLI tools for Short-Reads FASTA/FASTQ files preprocessing
wip/diffanal Fast, simple differential analysis
math/basic-stats Command-line tool to perform basic statistics on tabular data
wip/plasm Portable Assembler
wip/papp Assembly Preprocessor
wip/fasda Fast and simple differential analysis