dozy

crammer

Reference-based compression of SRA data

git-yacontrib

Assortment of useful scripts

hello-test

samtools-tests

Tests for samtools (including iRODS-specific tests)

bambi

A set of programs to manipulate SAM/BAM/CRAM files, using HTSLIB

baton

iRODS client programs and API

biobambam

Tools for bam file processing

htslib

C library for high-throughput sequencing data formats

libmaus

libmaus

ml_warehouse

Perl DBIx binding to a warehouse housing data from multiple LIM systems

npg_conda

NPG Conda recipes and tools

npg_irods

Tools for managing HTS (BAM and CRAM) format files in iRODS.

npg_ml_warehouse

Analysis results loader for the multi-lims warehouse, see ml_warehouse project for the warehouse details.

npg_qc

QC checks and metrics for Illumina NGS data

npg_seq_common

Utilities for handling NGS data

npg_seq_melt

Operations on processed sequencing data (merges, metadata updates for the archive, etc.)

npg_seq_pipeline

Processing and analysis of data coming from Illumina sequencing machines

npg_tracking

WTSI Illumina sequencing instruments (HiSeq, MiSeq, GA) tracking

p4

Process and Pipe Pipeline Panacea

pb_calibration

Filter and calibration programs for Illumina BAM files

perl-dnap-utilities

WTSI DNA Pipelines Perl Utility Library

perl-irods-wrap

Perl iRODS Client Wrapper Library

samtools

samtools_container

Scripts to create a docker container for samtools

vcftools

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