BioBuilds

biobuilds

Curated collection of open-source bioinformatics tools

bamkit

Tools for common BAM file manipulations

bowtie2

A fast and sensitive gapped read aligner

cufflinks

fastx_toolkit

FASTA/FASTQ pre-processing programs

libgtextutils

Gordon's Text utils Library

ncbi-vdb

ncbi-vdb

ngs

NGS Language Bindings

oases

De novo transcriptome assembler for short reads

plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Future development will revolve around critical extensions to the core file format (multiallelic variants, dosage, phase).

python3statement.github.io

SOAPdenovo2

Next generation sequencing reads de novo assembler.

sra-tools

SRA Tools

vcflib

a simple C++ library for parsing and manipulating VCF files, + many command-line utilities

bioperl-ext

XS-based BioPerl extensions to C libraries (defunct)

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

CEGMA_v2

The final version 2 release of our software to detect core genes in eukaryotic genomes

chimerascan

Automatically exported from code.google.com/p/chimerascan

docker

BioBuilds-related Docker images and utilities

gatk

Official code repository for GATK versions 4 and up