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10xqc

A system for monitoring the quality of 10X single cell data

artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

assembly-stats

Get assembly statistics from FASTA and FASTQ files

bamseqchksumjava

Prototype implementation of BAM checksumming in Java

baton

iRODS client programs and API

bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

bcviz

JavaScript visualisation for bamcheck file format

beetl

BEETL

biobambam

Tools for bam file processing

biobambam2

Tools for early stage alignment file processing

bowtie

An ultrafast memory-efficient short read aligner

bwtb3m

Burrows Wheeler Transform By Balanced Block Merging

bxtools

Tools for analyzing 10X genomics data

capmq

Simple program to cap mapping quality in a given alignment file

cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

demuxlet

Genetic multiplexing of barcoded single cell RNA-seq

disposable-irods

Scripts to create a minimal, disposable IRODS as a test platform

gastore

Sample code to inform a discussion around content-addressable storage

genotyping

Components of the WTSI genotype analysis pipeline.

hp4

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

htslib

C library for high-throughput sequencing data formats. This is the official repository.

htslib-plugins

Plugins for use with HTSlib

irods_resource_plugin_directaccess

Direct Access resource plugin for iRODS

isaac_aligner

Isaac Genome Alignment Software

ivar

kubespray

Setup a kubernetes cluster

lariat

Linked-Read Alignment Tool

libmaus

libmaus

libmaus2

collection of data structures and algorithms