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nvbio

NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA.

pb-assembly

PacBio Assembly Tool Suite: Reads in ⇨ Assembly out

pb_calibration

Filter and calibration programs for Illumina BAM files

pbccs

PacBio circular consensus sequencing

perl-irods-wrap

Perl iRODS Client Wrapper Library

picard

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.sourceforge.net) format.

pybedtools

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

pypop

Python for Population Genomics

pysam

Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

rt

Request Tracker, an enterprise-grade issue tracking system

samtools

MP15's working samtools repo (not official release expect rebases)

samtools_addreplacereadgroups

samtools_dev_env

Xcode dev environment for samtools

samtools_merge

scaff10x

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

seq_autoqc

Additional high-throughput sequencing autoQC steps

server

A reference implementation of the APIs defined in the schemas repository.

synergy-scheduler-manager

Provide advanced scheduling capability for OpenStack using a fairshare algorithm. This is a manager for synergy-service.

testweb

tsv2bin

Sanger SNP DB TSV to Hapmap and VCF converter

typeloader

untangle

variantworks

Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/

vcf_merge_annot

Merge vcf annotations from sites files

vr-codebase

The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute

vr-pipe

Generic pipeline system

wsl2-linux-kernel

The source for the Linux kernel used in Windows Subsystem for Linux 2 (WSL2)

zlib

Set up to contribute patches to intel's modifications to zlib