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bcftools

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

bedtools2

bedtools - the swiss army knife for genome arithmetic

bioqueue.github.io

bowtie2

A fast and sensitive gapped read aligner

cwltool

Common Workflow Language reference implementation

deeptools

Tools to process and analyze deep sequencing data.

dependent-packages-backup

fastp

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

gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF

hisat2

Graph-based alignment (Hierarchical Graph FM index)

pints

references

salmon

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

samtools

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

sra-tools

SRA Tools

star

RNA-seq aligner

tools

ucsc-tools

UCSC Genome Browser source tree. Stable branch: "beta".

umi-tools

Tools for handling Unique Molecular Identifiers in NGS data sets

wiggletools

Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency