The following packages were found for maintainer: bacon@netbsd.org
Restricting search to CURRENT branch. (Show all branches)

wip/salmon Transcript-level quantification of RNA-seq from lightweight alignments
wip/bwa Map low-divergent sequences against a large reference genome
wip/libbacon Miscellaneous experimental functions
wip/ape Another Programmers Editor
wip/pbcopper Core C++ library for data structures, algorithms, and utilities
biology/trimmomatic Flexible read trimming tool for Illumina NGS data
wip/ganglia-webfrontend PHP based frontend for the Ganglia Cluster Monitor
wip/gtextutils Gordon text utilities
wip/meep-openmpi FDTD simulation software to model electromagnetic systems
wip/fastahack Utilities for indexing and sequence extraction from FASTA files
wip/parafly Process the commands in parallel on a single server
wip/metal Meta-analysis of genomewide association scans
wip/py-ufl Unified Form Language for finite element discretizations
wip/pbbam PacBio BAM C++ library, with SWIG bindings
wip/vcftools Tools for working with VCF genomics files
wip/suitesparse SuiteSparse is a set of packages for sparse matrices calculation
wip/ddocent Bash pipeline for RAD sequencing
wip/mpb MIT Photonic Bands
wip/yaggo Generate command line parser using getopt_long
wip/daligner Find all significant local alignments between reads
wip/dlpoly-classic General purpose classical molecular dynamics
wip/py-rdflib340 Python library for RDF manipulation
wip/rsem RNA-Seq by Expectation-Maximization
wip/samtools Tools for manipulating sequence alignment maps
wip/man2html Convert nroff(1) man pages to HTML
wip/htslib C library for high-throughput sequencing data formats
biology/plinkseq C/C++ library for working with human genetic variation data
wip/cluster-admin HPC cluster admin tools
biology/plink Whole-genome association analysis toolset
wip/bolt-lmm Statistics for testing association between phenotype and genotypes
wip/py-viper Scientific plotter and run-time visualization module
wip/pear Memory-efficient and highly accurate pair-end read merger
wip/py-macs2 Novel algorithm for identifying transcript factor binding sites
wip/p5-trimgalore Wrapper around Cutadapt and FastQC for adapter and quality trimming
wip/fbsd2pkg Convert a FreeBSD port framework to a pkgsrc package
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/fftw-openmpi Collection of fast C routines to compute DFTs
wip/openmx-openmpi Nano-scale material simulations based on DFT
wip/dazz_db Dresden assembler for long read DNA projects
wip/gmap Genomic Mapping and Alignment Program for mRNA and EST Sequences
wip/fastaunique Sort and uniq fasta files
wip/py-pbfalcon Experimental PacBio diploid assembler
wip/p5-IPC-Open3-Simple Simple alternative to IPC::Open3
wip/linux-ukbgene Tool for accessing UK Biobank data
wip/haplohseq Identify regions of allelic imbalance
wip/blasr_libcpp Library for analyzing PacBio sequences
wip/tophat Fast splice junction mapper for RNA-Seq reads
wip/py-rdfextras Collection of packages providing extras based on RDFLib 3
wip/lmod Dynamic modification of a users environment
wip/detab Replace tabs with spaces in a text file
wip/hisat2 Alignment program for mapping next-generation sequencing reads
wip/blasr PacBio(R) long read aligner
wip/ad2vcf Add allelic depth info from a SAM stream to a VCF file
wip/twintk Terminal Windows Toolkit
wip/libpare Pointer Array Regular Expressions
wip/py-anvio Analysis and visualization platform for omics data
wip/libzeep Make it easy to create SOAP servers
wip/xssp Software for creating DSSP and HSSP files
wip/py-pysam Python module for reading, manipulating and writing genomic data sets
wip/R-optparse Command Line Option Parser
wip/vcf-split Split a multi-sample VCF into single-sample VCFs
wip/famsa Algorithm for large-scale multiple sequence alignments
wip/py-ete3 Python Environment for (phylogenetic) Tree Exploration
wip/py-snakemake Reduce the complexity of creating workflows
wip/py-eggnog-mapper Fast functional annotation of novel DNA or protein sequences
wip/optibench Benchmark to measure optimal sustained memory and disk performance
wip/R-getopt C-Like getopt Behavior
wip/fasttree Approximately-maximum-likelihood phylogenetic trees from alignments
textproc/man2html Convert nroff(1) man pages to HTML
wip/py-htseq Framework to analyze data from high-throughput sequencing assays
wip/ncbi-blast+ NCBI implementation of Basic Local Alignment Search Tool
wip/meep FDTD simulation software to model electromagnetic systems
wip/antlr ANother Tool for Language Recognition
wip/udunits2 Library for manipulating units of physical quantities
wip/plink Whole genome association analysis toolset
wip/seqtk Tool for processing sequences in FASTA/FASTQ format
wip/fftw-mpich Collection of fast C routines to compute DFTs
wip/filevercmp Filevercmp function as in sort --version-sort
wip/fsom Tiny C library for managing SOM (Self-Organizing Maps) neural networks
wip/slclust Single-linkage clustering with Jaccard similarity
biology/hisat2 Alignment program for mapping next-generation sequencing reads
wip/bpcscripts Gast Illumina processing
archivers/libaec Adaptive entropy coding library
wip/intervaltree Minimal C++ interval tree implementation
wip/kallisto Quantify abundances of transcripts from RNA-Seq data
wip/structure Multi-locus genotype data to investigate population structure
wip/jellyfish Fast, memory-efficient counting of k-mers in DNA
wip/R-mpfr Multiple Precision Floating Point Arithmetic for R
wip/mcl Fast and scalable unsupervised cluster algorithm for graphs
wip/tabixpp C++ wrapper to tabix indexer
wip/gromacs Molecular dynamics package
biology/ncbi-blast+ NCBI implementation of Basic Local Alignment Search Tool
wip/canu Single molecule sequence assembler for genomes large and small
wip/singularity Application container for Linux
wip/py-graph-tool Python module for manipulation and statistical analysis of graphs
wip/cereal C++11 library for serialization
wip/mpb-openmpi MIT Photonic Bands
wip/numactl Non Uniform Memory Access tools
wip/centrifuge Novel microbial classification engine
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
security/munge Authentication service for creating and validating credentials
biology/canu Single molecule sequence assembler for genomes large and small
biology/vsearch Versatile open-source tool for metagenomics
wip/openmpi Open source implementation
wip/p5-transdecoder Identify candidate coding regions within transcript sequences
biology/py-cutadapt Find and remove adapter sequences, primers, poly-A tails, etc
wip/subread High-performance read alignment, quantification and mutation discovery
math/udunits Library and program for manipulating units of physical quantities
biology/vcf-split Split a multi-sample VCF into single-sample VCFs
biology/stacks Software pipeline for building loci from short-read sequences
biology/fastp Ultra-fast all-in-one FASTQ preprocessor
devel/libctl Guile-based flexible control file library for scientific simulations
wip/auto-admin Portable tools for automating systems management
parallel/slurm-wlm Simple Linux Utility for Resource Management
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/biolibc Low-level high-performance bioinformatics library
textproc/R-data.table Extension of data.frame
wip/pbseqan PacBio patched and stripped down seqan
wip/armadillo C++ linear algebra library
wip/epacts Efficient and Parallelizable Association Container Toolbox
wip/py-fiat Finite element Automatic Tabulator
wip/meep-mpi FDTD simulation software to model electromagnetic systems
wip/cdbfasta Fast indexing and retrieval of fasta records from flat file databases
wip/basic-stats Command-line tool to perform basic statistics on tabular data
wip/py-hostlist Manage SLURM host lists
wip/cdhit Clustering and comparing protein or nucleotide sequences
wip/plink2 Whole genome association analysis toolset
wip/hmmer Profile hidden Markov models for biological sequence analysis
wip/vcf2hap Generate .hap file from VCF for haplohseq
wip/ufc Unified framework for finite element assembly
wip/py-ffc C++ code generator for multilinear forms
wip/smithwaterman Smith-waterman-gotoh alignment algorithm
devel/swig2 Simplified Wrapper and Interface Generator (version 2)
wip/prodigal Prokaryotic Dynamic Programming Genefinding Algorithm
wip/fastx-toolkit CLI tools for Short-Reads FASTA/FASTQ files preprocessing
wip/igv Visualization tool for genomic datasets
biology/igv Visualization tool for genomic datasets
wip/fastool Simple and quick FastQ and FastA tool for file reading and conversion
wip/gromacs2018 Molecular dynamics package
wip/munge Authentication service for creating and validating credentials
wip/gemma Genome-wide Efficient Mixed Model Association
wip/trinity Assembles transcript sequences from Illumina RNA-Seq data
biology/samtools Tools for manipulating sequence alignment maps
wip/rainbow Short reads clustering and local assembly
biology/py-dnaio Read and write FASTQ and FASTA files
biology/htslib C library for high-throughput sequencing data formats
wip/py-dnaio Read and write FASTQ and FASTA files
devel/R-rematch Match regular expressions with a nicer API
wip/generand Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
wip/unanimity Consensus library and applications
wip/libaec Adaptive entropy coding library
wip/fvcom2 Prognostic coastal ocean circulation model
wip/tbb Library that provides thread building blocks
parallel/ganglia-monitor-core Ganglia cluster monitor, monitoring daemon
biology/generand Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
biology/biolibc Low-level high-performance bioinformatics library
biology/ad2vcf Add allelic depth info from a SAM stream to a VCF file
biology/vcf2hap Generate .hap file from VCF for haplohseq
wip/docviewer Generic command to automatically select a document viewer
wip/webbrowser Proxy script for launching best available web browser
wip/wgrib2 Tools for managing GRIB weather data files
wip/wip-tools Tools for developing wip packages
wip/bowtie Ultrafast, memory-efficient short read aligner
textproc/R-cellranger Translate spreadsheet cell ranges to rows and columns
wip/vsearch Versatile open-source tool for metagenomics
wip/fastp Ultra-fast all-in-one FASTQ preprocessor
wip/spcm Simple, portable cluster management
wip/bcftools Tools for manipulating BCF and VCF variant call files
wip/runas Wrapper around su for running a command as another user
wip/peak-classifier Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
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/pkg-dev Scripts to automate common tasks in pkgsrc development
wip/pooler Optimise DNA sequencing primer-set combinations
sysutils/auto-admin Portable tools for automating systems management
wip/py-pypeflow Lightweight and reusable make/flow data process library
wip/libxtend Miscellaneous functions to extend libc
wip/py-biopython Collection of Python modules for bioinformatics
biology/bowtie2 Ultrafast, memory-efficient short read aligner
devel/py-xopen Open compressed files transparently
biology/bedtools Swiss army knife for genome arithmetic
wip/bedtools Swiss army knife for genome arithmetic
wip/jellyfish2 Fast, memory-efficient counting of k-mers in DNA