Wellcome Sanger Institute - NPG

Login: wtsi-npg

Company: null

Location: Cambridge UK

email:

Blog: www.sanger.ac.uk

Members

1. Jennifer Liddle
2. Keith James
3. Kevin Lewis
4. Ruben E. Bautista
5. null
6. null
7. null

Repositories

AnyEvent-RabbitMQ

An asynchronous and multi channel Perl AMQP client.

bambamc

lightweight C implementation of name collating BAM file input and BAM file output

bambi

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

baton

iRODS client programs and API

bcviz

JavaScript visualisation for bamcheck file format

biobambam

Tools for bam file processing

bwa

Burrows-Wheeler Aligner

crammer

Reference-based compression of SRA data

dalliance

Interactive web-based genome browser.

disposable-irods

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

freebayes

Bayesian haplotype-based polymorphism discovery and genotyping.

genotype-call

Explore the contents of Illumina's binary Genotype Call files

genotyping

Components of the WTSI genotype analysis pipeline.

Gftools

A set of utilities to handle individual-level genotype data files

git-pom-version

Updates the version of Maven pom files using "git describe"

hp4

null

htslib

C library for high-throughput sequencing data formats

illumina2bam

Generate and process BAM files from Illumina sequencing instrument files

Illuminus

A genotype calling algorithm for the Illumina BeadArray platform

irods

Middleware for your critical data.

irods-legacy

Fork of DICE irods-legacy

irods-legacy-gclp

This repository mirrors the legacy DICE-UCSD iRODS SVN repository at this time. No pull-requests will be merged back into trunk.

irods-metadata

Description of a subset of metadata used in WTSI iRODS

ml_warehouse

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

npg_conda

NPG Conda recipes and tools

npg_docker

Prototypes of Docker-contained Pipelines

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_qc_utils

C programs extracted from npg_qc

npg_ranger

NGS data streaming (sam, bam, cram, vcf) - pre-production

npg_sentry

null

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_sequencescape_warehouse

Old sequencescape warehouse: DBIx binding, loader, LIMs driver for st::api::lims

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

Percolate

A parallel workflow management application.

perl-dnap-utilities

WTSI DNA Pipelines Perl Utility Library

perl-irods-wrap

Perl iRODS Client Wrapper Library

perl-rabbit-wrap

Perl RabbitMQ Client Wrapper Library (deprecated)

plinktools

Process Plink genotyping files in Python

samtools

null

samtools-patches

patch files for various releases of samtools

simtools

Program to create and process SIM files

teepot

null

unveil

A very lightweight jQuery plugin to lazy load images

vcftools

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

zCall

A Rare Variant Caller for Array-based Genotyping