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

Official code repository for GATK versions 4 and up

RNA-seq aligner

Spliced read mapper for RNA-Seq

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

A fast and sensitive gapped read aligner

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Aggregate results from bioinformatics analyses across many samples into a single report.

A quality control analysis tool for high throughput sequencing data

Tools (written in C using htslib) for manipulating next-generation sequencing data

bedtools - the swiss army knife for genome arithmetic

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Near-optimal RNA-Seq quantification

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)