This project was created for package R-StanHeaders via attribute OBS:Maintained

This project was created for package R-rstan via attribute OBS:Maintained

This project was created for package rkward6 via attribute OBS:Maintained

Packaging scientific (e.g. bioinformatics) software

Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.

Package for the new BCFtools: a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. It contains all the "vcf..." commands which previously lived in the HTSlib repository (such as vcfcheck, vcfmerge, vcfisec, etc.) and the samtools BCF calling from bcftools subdirectory of samtools. BCFtools are meant as a faster replacement for most of the perl VCFtools commands.

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.

JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. JAGS was written with three aims in mind:

- To have a cross-platform engine for the BUGS language
- To be extensible, allowing users to write their own functions, distributions and samplers.
- To be a platform for experimentation with ideas in Bayesian modelling

HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools.

HTSlib implements a generalized BAM index, with file extension .csi (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent.

This project also includes the popular tabix indexer, which indexes both .tbi and .csi formats, and the bgzip compression utility.

Spliced Transcripts Alignment to a Reference © Alexander Dobin, 2009-2019 https://www.ncbi.nlm.nih.gov/pubmed/23104886

Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.

Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.

This is the legacy version which does not use the HTSlib and is required by some software.

Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.