Idea Transcript
Github Conglomerate This project isn't endorsed by anyone, especially Github. Some organisations split their code across a number of Github organisations; this project brings it back together. Naturally it's hosted on Github (https://github.com/bewt85/GithubConglomerate), your help making it better would be warmly received. For example, if you can lend some bootstrap or think of a better scoring algorithm (https://github.com/bewt85/GithubConglomerate/blob/master/github_conglomerate/Views.py), please feel free to make a pull request
Organisation
Repo
Description
sco
samtools
samtools (https://github.com/samtools/samtools)
Tools (written in C using htslib) for manipulating next-generation sequencing data
25.8
samtools
htsjdk (https://github.com/samtools/htsjdk)
A Java API for high-throughput sequencing data (HTS) formats.
25.0
samtools
htslib (https://github.com/samtools/htslib)
C library for high-throughput sequencing data formats
23.4
samtools
bcftools (https://github.com/samtools/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
19.7
samtools
hts-specs (https://github.com/samtools/hts-specs)
Specifications of SAM/BAM and related high-throughput sequencing file formats
18.7
wtsi-web
Genoverse (https://github.com/wtsi-web/Genoverse)
HTML5 scrollable genome browser
17.3
sanger-pathogens
iva (https://github.com/sanger-pathogens/iva)
de novo virus assembler of Illumina paired reads
16.4
samtools
tabix (https://github.com/samtools/tabix)
Note: tabix and bgzip binaries are now part of the HTSlib project.
15.3
sanger-pathogens
circlator (https://github.com/sanger-pathogens/circlator)
A tool to circularize genome assemblies
14.8
sanger-pathogens
Artemis (https://github.com/sanger-pathogens/Artemis)
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
14.8
sanger
sequencescape (https://github.com/sanger/sequencescape)
Web based Lims
14.2
VertebrateResequencing
vr-codebase (https://github.com/VertebrateResequencing/vrcodebase)
The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute
13.8
sanger-pathogens
Fastaq (https://github.com/sanger-pathogens/Fastaq)
Python3 scripts to manipulate FASTA and FASTQ files
13.1
VertebrateResequencing
vr-pipe (https://github.com/VertebrateResequencing/vr-pipe)
Generic pipeline system
13.0
wtsi-hgi
docker-proxify (https://github.com/wtsi-hgi/docker-proxify)
Allows building and running docker container images from behind a corporate proxy
12.8
wtsi-npg
illumina2bam (https://github.com/wtsi-npg/illumina2bam)
Generate and process BAM files from Illumina sequencing instrument files
12.4
wtsi-ssg
pcp (https://github.com/wtsi-ssg/pcp)
Parallel copy tool
12.2
wtsi-npg
p4 (https://github.com/wtsi-npg/p4)
Process and Pipe Pipeline Panacea
12.1
cancerit
CaVEMan (https://github.com/cancerit/CaVEMan)
SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib
12.0
wtsi-npg
baton (https://github.com/wtsi-npg/baton)
iRODS client programs and API
11.7
sanger-pathogens
GeneDB (https://github.com/sanger-pathogens/GeneDB)
Web front-end for genomic data, developed at the Pathogen Genomics group, Wellcome Trust Sanger Institute
10.9
wtsi-npg
Percolate (https://github.com/wtsi-npg/Percolate)
A parallel workflow management application.
10.7
sanger
warehouse_two (https://github.com/sanger/warehouse_two)
Denormalised warehouse for Sequencescape
10.7
sanger-pathogens
Roary (https://github.com/sanger-pathogens/Roary)
Pan genome pipeline
10.4
cancerit
ascatNgs (https://github.com/cancerit/ascatNgs)
Somatic copy number analysis using paired end sequencing
10.4
sanger-pathogens
vr-codebase (https://github.com/sanger-pathogens/vrcodebase)
The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute
10.2
sanger
sequencescape-client-api (https://github.com/sanger/sequencescape-client-api)
Ruby gem for the interacting with the sequencescape API.
10.2
sanger
lims-core (https://github.com/sanger/lims-core)
Core of the new LIMS
10.2
cancerit
cgpPindel (https://github.com/cancerit/cgpPindel)
Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel
10.0
sanger-pathogens
deployment (https://github.com/sangerpathogens/deployment)
cancerit
alleleCount (https://github.com/cancerit/alleleCount)
Support code for NGS copy number algorithms
9.87
sanger-pathogens
snp_sites (https://github.com/sanger-pathogens/snp_sites)
Finds SNP sites from a multi fasta alignment file
9.87
sanger-pathogens
Web-Artemis (https://github.com/sanger-pathogens/WebArtemis)
wtsi-npg
perl-irods-wrap (https://github.com/wtsi-npg/perl-irods-wrap)
Perl iRODS Client Wrapper Library
9.48
sanger-pathogens
crawl2 (https://github.com/sanger-pathogens/crawl2)
A spiritual successor to Crawl
9.43
sanger
lims-api (https://github.com/sanger/lims-api)
The API for the new LIMS
9.39
sanger-pathogens
gubbins (https://github.com/sanger-pathogens/gubbins)
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
9.39
sanger-pathogens
update_pipeline (https://github.com/sangerpathogens/update_pipeline)
wtsi-npg
bcviz (https://github.com/wtsi-npg/bcviz)
JavaScript visualisation for bamcheck file format
9.10
wtsi-npg
simtools (https://github.com/wtsi-npg/simtools)
Program to create and process SIM files
8.99
sanger-pathogens
assembly_improvement (https://github.com/sangerpathogens/assembly_improvement)
cancerit
cgpCaVEManWrapper (https://github.com/cancerit/cgpCaVEManWrapper)
Reference implementation of CGP workflow for CaVEMan SNV analysis
8.64
cancerit
cgpBattenberg (https://github.com/cancerit/cgpBattenberg)
Battenberg algorithm and associated implementation script
8.37
wtsi-npg
genotyping (https://github.com/wtsi-npg/genotyping)
Components of the WTSI genotype analysis pipeline.
8.37
wtsi-hgi
ep_sotauth (https://github.com/wtsi-hgi/ep_sotauth)
Etherpad Lite plugin to trust authentication passed in from XForwarded-User HTTP header. This is useful when running behind a reverse proxy (a "series of tubes") that handles authentication. Do not use this plugin unless you have protected the server so that it can only be accessed from the reverse proxy.
8.37
sanger
pulldown_pipeline (https://github.com/sanger/pulldown_pipeline)
The UI application for the Pulldown pipeline
8.22
cancerit
BRASS (https://github.com/cancerit/BRASS)
BReakpoint AnalySiS - Identifies breaks and attempts to assemble rearrangements.
8.14
sanger-pathogens
ariba (https://github.com/sanger-pathogens/ariba)
Antibiotic Resistance Identification By Assembly
8.14
wtsi-npg
perl-dnap-utilities (https://github.com/wtsi-npg/perl-dnaputilities)
WTSI DNA Pipelines Perl Utility Library
7.89
wtsi-npg
npg_docker (https://github.com/wtsi-npg/npg_docker)
Prototypes of Docker-contained Pipelines
7.89
sanger-pathogens
assembly-stats (https://github.com/sangerpathogens/assembly-stats)
Get assembly statistics from FASTA and FASTQ files
7.89
wtsi-npg
pb_calibration (https://github.com/wtsi-npg/pb_calibration)
Filter and calibration programs for Illumina BAM files
7.60
sanger-pathogens
mlst_check (https://github.com/sanger-pathogens/mlst_check)
wtsi-clarity
wtsi_clarity (https://github.com/wtsi-clarity/wtsi_clarity)
Custom scripting for Clarity LIMS (http://www.genologics.com) at Wellcome Trust Sanger Institute
7.49
Anacode
cvs2git-wrap (https://github.com/Anacode/cvs2git-wrap)
Exposed: the cvs2git process we used for ensembl-otter
7.49
wtsi-npg
Gftools (https://github.com/wtsi-npg/Gftools)
A set of utilities to handle individual-level genotype data files
7.49
samtools
www.htslib.org (https://github.com/samtools/www.htslib.org)
The http://www.htslib.org/ web site
7.26
wtsi-npg
irods (https://github.com/wtsi-npg/irods)
Middleware for your critical data.
7.26
wtsi-npg
npg_qc (https://github.com/wtsi-npg/npg_qc)
QC checks and metrics for Illumina NGS data
7.26
sanger
asset_audits (https://github.com/sanger/asset_audits)
Add audits to assets in sequencescape
7.26
sanger-pathogens
json2email (https://github.com/sanger-pathogens/json2email)
Takes a jinja2 template and some json and sends an email
7.26
sanger-pathogens
setup_tracking (https://github.com/sangerpathogens/setup_tracking)
setup a vrtracking pipeline
7.26
sanger
illumina_b_pipeline (https://github.com/sanger/illumina_b_pipeline)
UI application for a high volume Illumina - Beckman pipeline
6.87
sanger-pathogens
annot-nf (https://github.com/sanger-pathogens/annot-nf)
Eukaryotic genome annotation pipeline implemented in Nextflow
6.87
sanger-pathogens
gff3toembl (https://github.com/sanger-pathogens/gff3toembl)
Convert a GFF3 file to a format acceptable for submission to EMBL
6.87
sanger-pathogens
pymummer (https://github.com/sanger-pathogens/pymummer)
Python3 module for running MUMmer and reading the output
6.87
wtsi-hgi
bridgebuilder (https://github.com/wtsi-hgi/bridgebuilder)
BridgeBuilder efficiently remaps BAM/SAM reads to a new reference by first building a "bridge" reference, first mapping to that bridge, and then remapping only a subset of reads to the full new reference.
6.87
wtsi-npg
npg_seq_pipeline (https://github.com/wtsinpg/npg_seq_pipeline)
Processing and analysis of data coming from Illumina sequencing machines
6.72
sanger-pathogens
MIDAS (https://github.com/sanger-pathogens/MIDAS)
Front end for the HICF pathogen genome store
6.72
sanger
acts-as-dag (https://github.com/sanger/acts-as-dag)
Directed Acyclic Graph hierarchy for Rail's ActiveRecord models
6.38
sanger-pathogens
crawl (https://github.com/sanger-pathogens/crawl)
Chado Restful Access Webservice Layer
6.38
wtsi-npg
irods-legacy (https://github.com/wtsi-npg/irods-legacy)
Fork of DICE irods-legacy
6.38
sanger-pathogens
reference_track (https://github.com/sangerpathogens/reference_track)
wtsi-npg
npg_tracking (https://github.com/wtsi-npg/npg_tracking)
WTSI Illumina sequencing instruments (HiSeq, MiSeq, GA) tracking
5.99
sanger
S2Mapper (https://github.com/sanger/S2Mapper)
AMD module to map an S2 API
5.99
sanger
lims-support-app (https://github.com/sanger/lims-support-app)
Application supporting the LIMS functionality
5.99
sanger-pathogens
bragv (https://github.com/sanger-pathogens/bragv)
cancerit
cgpCaVEManPostProcessing (https://github.com/cancerit/cgpCaVEManPostProcessing)
Flagging add on to CaVEMan
5.76
Anacode
ensembl-otter (https://github.com/Anacode/ensembl-otter)
The Otterlace genome annotation editor, and supporting code
5.76
wtsi-npg
npg_seq_common (https://github.com/wtsinpg/npg_seq_common)
Utilities for handling NGS data
5.76
wtsi-npg
perl-rabbit-wrap (https://github.com/wtsi-npg/perl-rabbit-wrap)
Perl RabbitMQ Client Wrapper Library
5.76
wtsi-medical-genomics
evoker (https://github.com/wtsi-medical-genomics/evoker)
Evoker is a graphical tool for plotting genotype intensity data in order to assess quality of genotype calls. It implements a compact, binary format which allows rapid access to data, even with hundreds of thousands of observations.
5.76
sanger
s2_extraction_pipeline (https://github.com/sanger/s2_extraction_pipeline)
A lab pipeline application for DNA and/or RNA extraction workflows
5.76
sanger-pathogens
Assembly_tools (https://github.com/sangerpathogens/Assembly_tools)
Scripts relating to genome assemblies
5.76
sanger-pathogens
Bio-Tradis (https://github.com/sanger-pathogens/Bio-Tradis)
cancerit
cgpVcf (https://github.com/cancerit/cgpVcf)
Vcf file utilities
5.51
cancerit
VAGrENT (https://github.com/cancerit/VAGrENT)
A toolset for comparing genomic variants to reference genome annotation to identify potential biological consequences
5.51
wtsi-npg
Illuminus (https://github.com/wtsi-npg/Illuminus)
A genotype calling algorithm for the Illumina BeadArray platform
5.51
sanger
delayed_job_monitor (https://github.com/sanger/delayed_job_monitor)
Display the number of delayed jobs pending
5.51
wtsi-hgi
DNG_dev (https://github.com/wtsi-hgi/DNG_dev)
HGI's current version of DenovoGear, not the official release. A 5.51 program to detect denovo-variants using next-generation sequencing data. (http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html)
wtsi-npg
plinktools (https://github.com/wtsi-npg/plinktools)
Process Plink genotyping files in Python
5.51
sanger
lims-laboratory-app (https://github.com/sanger/limslaboratory-app)
Main S2 application (base on lims-core and lims-api)
5.51
sanger
training-repository (https://github.com/sanger/trainingrepository)
Repository for training new developers on our branching model.
5.51
sanger
user_barcode (https://github.com/sanger/user_barcode)
Sinatra app to translate a scanned user barcode into a username
5.51
sanger-pathogens
Bio-RNASeq (https://github.com/sanger-pathogens/BioRNASeq)
The new Sanger Pathogen Informatics RNA Seq analysis pipeline
5.51
sanger-pathogens
Farm_blast (https://github.com/sanger-pathogens/Farm_blast) Python3 module to run blast+ or blastall in parallel on an LSF compute farm
5.51
sanger-pathogens
PathFind (https://github.com/sanger-pathogens/PathFind)
5.22
wtsi-npg
samtools_irods (https://github.com/wtsi-npg/samtools_irods)
4.99
sanger-pathogens
Bio-ENA-DataSubmission (https://github.com/sangerpathogens/Bio-ENA-DataSubmission)
4.99
sanger-pathogens
Bio-Metagenomics (https://github.com/sanger-pathogens/BioMetagenomics)
4.99
wtsi-npg
bwa (https://github.com/wtsi-npg/bwa)
Burrow-Wheeler Aligner
4.88
wtsi-npg
genotype-call (https://github.com/wtsi-npg/genotype-call)
Explore the contents of Illumina's binary Genotype Call files
4.88
wtsi-npg
ml_warehouse (https://github.com/wtsi-npg/ml_warehouse)
Perl DBIx binding to a warehouse housing data from multiple LIM systems
4.88
sanger
alter_table (https://github.com/sanger/alter_table)
Gem to add multiple alterations in one ALTER TABLE statement for 4.88 Rails migrations
sanger
labware (https://github.com/sanger/labware)
A collection of HTML, CSS and images that can be used to represent laboratory equipment
4.88
sanger
lims-management-app (https://github.com/sanger/limsmanagement-app)
S2 sample management
4.88
sanger
plate_barcode (https://github.com/sanger/plate_barcode)
Get a barcode for a plate
4.88
sanger
sanger_barcode (https://github.com/sanger/sanger_barcode)
A gem to use and print sanger barcode
4.88
sanger
sm_workflow_lims (https://github.com/sanger/sm_workflow_lims)
A small Lims to assist with managing workflows
4.88
sanger-pathogens
bio_assembly_refinement (https://github.com/sangerpathogens/bio_assembly_refinement)
Tools to refine/finish an assembly
4.88
sanger-pathogens
citation_reporter (https://github.com/sangerpathogens/citation_reporter)
Website to show your team's publications (which are in PubMed)
4.88
wtsi-hgi
IYG (https://github.com/wtsi-hgi/IYG)
Inside Your Genome Project
4.88
wtsi-hgi
nodervisor (https://github.com/wtsi-hgi/nodervisor)
Supervisor manager in node.js
4.88
sanger-pathogens
find_files_for_deletion (https://github.com/sangerpathogens/find_files_for_deletion)
4.76
sanger-pathogens
pipelines_reporting (https://github.com/sangerpathogens/pipelines_reporting)
4.76
sanger-pathogens
vrtrack_crawl (https://github.com/sangerpathogens/vrtrack_crawl)
4.76
sanger
cluster_view (https://github.com/sanger/cluster_view)
4.51
sanger-pathogens
Bio-InterProScanWrapper (https://github.com/sangerpathogens/Bio-InterProScanWrapper)
4.51
sanger-pathogens
Bio-VertRes-Config (https://github.com/sangerpathogens/Bio-VertRes-Config)
4.51
cancerit
cgpNgsQc (https://github.com/cancerit/cgpNgsQc)
Collection of code for checking NSG sequencing results
4.49
sanger
usg_scripts (https://github.com/sanger/usg_scripts)
Sequencescape Lims user support scripts
4.49
sanger-pathogens
Bio-AutomatedAnnotation (https://github.com/sangerpathogens/Bio-AutomatedAnnotation)
Perl module to take in an genomic assembly and produce annoation
4.49
cancerit
cgpBinCounts (https://github.com/cancerit/cgpBinCounts)
Generates bin count files as required by PICNIC-NGS and some other tools
4.00
cancerit
grass (https://github.com/cancerit/grass)
Gene Rearrangement AnalySiS
4.00
cancerit
WwDocker (https://github.com/cancerit/WwDocker)
(WildWest) Docker - Docker host manager using RabbitMQ
4.00
wtsi-npg
git-pom-version (https://github.com/wtsi-npg/git-pom-version)
Updates the version of Maven pom files using "git describe"
4.00
wtsi-npg
npg_ml_warehouse (https://github.com/wtsinpg/npg_ml_warehouse)
Analysis results loader for the multi-lims warehouse, see ml_warehouse project for the warehouse details.
4.00
wtsi-npg
zCall (https://github.com/wtsi-npg/zCall)
A Rare Variant Caller for Array-based Genotyping
4.00
VertebrateResequencing
pbwt (https://github.com/VertebrateResequencing/pbwt)
Implementation of Positional Burrows-Wheeler Transform for genetic data
4.00
wtsi-medical-genomics
phenodb (https://github.com/wtsi-medical-genomics/phenodb) Database and web based interface for recording phenotype and sample information for individuals involved in genetic studies information, developed using Python and Django.
4.00
sanger
activerecord-partitioning (https://github.com/sanger/activerecord-partitioning)
Add support for partitioned tables to ActiveRecord
4.00
sanger
asset_location (https://github.com/sanger/asset_location)
The freezer location of a piece of labware(plate/tube)
4.00
sanger
irods_reader (https://github.com/sanger/irods_reader)
A simple wrapper interface for the iRods command line tools
4.00
sanger-pathogens
Bio-Metadata-Validator (https://github.com/sangerpathogens/Bio-Metadata-Validator)
Validate a genome metadata manifest against a checklist
4.00
sanger-pathogens
PathPipeConfTools (https://github.com/sangerpathogens/PathPipeConfTools)
Outputs details of all of the pathogen jobs in the pipeline
4.00
wtsi-hgi
serapis (https://github.com/wtsi-hgi/serapis)
Serapis archival system
4.00
wtsi-hgi
sharelatex (https://github.com/wtsi-hgi/sharelatex)
A web-based collaborative LaTeX editor
4.00
wtsi-hgi
tabula (https://github.com/wtsi-hgi/tabula)
Project logging and analysis in the console.
4.00
wtsi-hgi
www-hierarchical-fairshare (https://github.com/wtsi-hgi/wwwhierarchical-fairshare)
Tools to view LSF hierarchical fairshare UserGroup shares and current priority (e.g. in a treemap)
4.00
sanger
lims-bridge-app (https://github.com/sanger/lims-bridge-app)
3.88
sanger-pathogens
annotation_store (https://github.com/sangerpathogens/annotation_store)
3.88
sanger-pathogens
gap5_consistency_checker (https://github.com/sangerpathogens/gap5_consistency_checker)
3.88
sanger-pathogens
QUASR (https://github.com/sanger-pathogens/QUASR)
3.88
sanger-pathogens
resistome-db (https://github.com/sangerpathogens/resistome-db)
3.88
wtsi-hgi
hgi-web (https://github.com/wtsi-hgi/hgi-web)
3.88
sanger
unified_warehouse (https://github.com/sanger/unified_warehouse)
3.49
samtools
sapi (https://github.com/samtools/sapi)
Sequence Alignment Programming Interface
3.38
cancerit
TraFiC (https://github.com/cancerit/TraFiC)
Transposable element detection
3.38
wtsi-npg
samtools-patches (https://github.com/wtsi-npg/samtoolspatches)
patch files for various releases of samtools
3.38
sanger
illumina_c_pipeline (https://github.com/sanger/illumina_c_pipeline)
Generic pipeline tool for plate managed library preparation
3.38
sanger
labwhere (https://github.com/sanger/labwhere)
A tool for tracking uniquely barcoded labware
3.38
sanger
lims-api-pulldown-mock (https://github.com/sanger/lims-apipulldown-mock)
Mock of lims-api needed to run the pulldown application using.
3.38
sanger
lims-auditor (https://github.com/sanger/lims-auditor)
Auditing application for S2
3.38
sanger
xultree (https://github.com/sanger/xultree)
XUL based JSON data viewer
3.38
sanger-pathogens
BioPericles (https://github.com/sangerpathogens/BioPericles)
A work in progress. BioPericles is designed to use supervised Machine Learning techniques to classify samples into clusters
3.38
sanger-pathogens
fasta_grep (https://github.com/sanger-pathogens/fasta_grep)
Efficiently pull filter FASTA files
3.38
sanger-pathogens
fastml (https://github.com/sanger-pathogens/fastml)
Addtional functionality for fastml, see http://fastml.tau.ac.il
3.38
sanger-pathogens
pathogens-vm (https://github.com/sangerpathogens/pathogens-vm)
To build a virtual machine with some Sanger pathogens software installed
3.38
sanger-pathogens
project-track (https://github.com/sanger-pathogens/projecttrack)
Track information about sequencing projects using ecap database
3.38
sanger-pathogens
rapid_annotation_transfer_tool (https://github.com/sangerpathogens/rapid_annotation_transfer_tool)
RATT: A tool for transferring genomic annotations between genomes
3.38
wtsi-hgi
cronic (https://github.com/wtsi-hgi/cronic)
A cure for Cron's chronic email problem
3.38
wtsi-hgi
hgi-project (https://github.com/wtsi-hgi/hgi-project)
HGI Project tracking database
3.38
sanger
lims-order-management-app (https://github.com/sanger/limsorder-management-app)
3.00
sanger
lims-warehousebuilder (https://github.com/sanger/limswarehousebuilder)
3.00
sanger
s2_skeleton (https://github.com/sanger/s2_skeleton)
3.00
sanger-pathogens
remove_blocks_from_aln (https://github.com/sangerpathogens/remove_blocks_from_aln)
3.00
samtools
samtools.github.com (https://github.com/samtools/samtools.github.com)
The http://samtools.github.io/ (master) and legacy http://samtools.sourceforge.net/ (sf-pages) web sites
2.50
wtsi-ssg
lustre_precise_build (https://github.com/wtsissg/lustre_precise_build)
A packer build for a compile machine for lustre
2.50
wtsi-ssg
pwalk (https://github.com/wtsi-ssg/pwalk)
Parallel filesystem walking utilities and library.
2.50
Anacode
cron2rss (https://github.com/Anacode/cron2rss)
Programs for watching cron job output via rss
2.50
Anacode
ensembl-otter-CVSbranches (https://github.com/Anacode/ensembl-otter-CVSbranches)
The Otterlace genome annotation editor, and supporting code. This repository contains the historic branches from CVS; branch structure is ambiguous in places.
2.50
wtsi-npg
AnyEvent-RabbitMQ (https://github.com/wtsi-npg/AnyEventRabbitMQ)
An asynchronous and multi channel Perl AMQP client.
2.50
wtsi-npg
biobambam (https://github.com/wtsi-npg/biobambam)
Tools for bam file processing
2.50
wtsi-npg
crammer (https://github.com/wtsi-npg/crammer)
Reference-based compression of SRA data
2.50
wtsi-npg
irods-metadata (https://github.com/wtsi-npg/irods-metadata)
Description of a subset of metadata used in WTSI iRODS
2.50
VertebrateResequencing
fastqcheck (https://github.com/VertebrateResequencing/fastqcheck)
Generate statistics on and validate fastq files
2.50
sanger
activerecord-triggers (https://github.com/sanger/activerecordtriggers)
Adds the ability to create and destroy triggers in ActiveRecord
2.50
sanger
ci_reporter (https://github.com/sanger/ci_reporter)
CI::Reporter is an add-on to Test::Unit and RSpec that allows you to generate XML reports of your test and/or spec runs.
2.50
sanger
crier (https://github.com/sanger/crier)
A very simple application for providing a range of notifications
2.50
sanger
freezer_tracking (https://github.com/sanger/freezer_tracking)
System for tracking labware in freezers
2.50
sanger
gatekeeper (https://github.com/sanger/gatekeeper)
The Tag QC Tool is used to track the production and validation of batches of tag plates for Sequencing. It is designed to interface with the LIMS Sequencescape.
2.50
sanger
lims-emailnotifier-app (https://github.com/sanger/limsemailnotifier-app)
lims-emailnotifier-app
2.50
sanger
manifest_merger_service (https://github.com/sanger/manifest_merger_service)
Single purpose Sinatra app to merge Excel and CSV data returning a new Excel spreadsheet
2.50
sanger
psd_logger (https://github.com/sanger/psd_logger)
Sanger/PSD specific modifications to SyslogLogger, a Ruby Logger replacement.
2.50
sanger
rack_authentication_sso (https://github.com/sanger/rack_authentication_sso)
Rack middleware to abstract Sanger SSO
2.50
sanger
rails_templates (https://github.com/sanger/rails_templates)
Rails application templates used by WTSI PSD team
2.50
sanger
ruby_walk (https://github.com/sanger/ruby_walk)
provide a customable map like function to explore any tree
2.50
sanger
s2-api-examples (https://github.com/sanger/s2-api-examples)
Examples, both JSON and code, of using the S2 API
2.50
sanger
s2_admin (https://github.com/sanger/s2_admin)
An admin interface for the S2 LIMS
2.50
sanger
stomp (https://github.com/sanger/stomp)
A ruby gem for sending and receiving messages from a Stomp protocol compliant message queue. Includes: failover logic, ssl support.
2.50
sanger
submission (https://github.com/sanger/submission)
Submission application built on the API
2.50
sanger
swipecard_manager (https://github.com/sanger/swipecard_manager)
An application to store a user swipecard code to Sequencescape.
2.50
sanger-pathogens
annot-web (https://github.com/sanger-pathogens/annot-web)
Web interface for annotation pipeline
2.50
sanger-pathogens
Farmpy (https://github.com/sanger-pathogens/Farmpy)
Python3 package to handle job submission to a compute farm
2.50
sanger-pathogens
iva-publication (https://github.com/sanger-pathogens/ivapublication)
Supplementary scripts and data for the IVA publication
2.50
sanger-pathogens
validate_tools (https://github.com/sangerpathogens/validate_tools)
File validation scripts and tools
2.50
sanger-pathogens
vr-pipe (https://github.com/sanger-pathogens/vr-pipe)
Generic pipeline system
2.50
wtsi-hgi
ep_disable_lists (https://github.com/wtsi-hgi/ep_disable_lists)
Etherpad Lite plugin to disable list/indentation controls.
2.50
wtsi-hgi
ep_pubmed (https://github.com/wtsi-hgi/ep_pubmed)
Etherpad Lite plugin to enable pubmed: identifiers (linking automatically to http://ncbi.nlm.nih.gov/pubmed/)
2.50
wtsi-hgi
gatk (https://github.com/wtsi-hgi/gatk)
GATK Official Release Repository: contains the core MIT-licensed GATK framework, free for all uses
2.50
wtsi-hgi
hgi-ansible (https://github.com/wtsi-hgi/hgi-ansible)
Ansible playbooks to manage hgi systems
2.50
wtsi-hgi
hgquota (https://github.com/wtsi-hgi/hgquota)
Tools for Sanger humgen users to find out information about available disk quota.
2.50
wtsi-hgi
json (https://github.com/wtsi-hgi/json)
JSON for Modern C++
2.50
wtsi-hgi
ldapvi (https://github.com/wtsi-hgi/ldapvi)
Clone of ldapvi from http://www.lichteblau.com/git/ldapvi.git
2.50
wtsi-hgi
mercury (https://github.com/wtsi-hgi/mercury)
Overarching repository for work on Mercury.
2.50
wtsi-hgi
redsocks (https://github.com/wtsi-hgi/redsocks)
transparent redirector of any TCP connection to proxy (unofficial copy)
2.50
wtsi-hgi
seq_autoqc (https://github.com/wtsi-hgi/seq_autoqc)
Additional high-throughput sequencing autoQC steps
2.50
wtsi-hgi
shadowbroker (https://github.com/wtsi-hgi/shadowbroker)
Quick tool to connect the HGI queues on RT to the MUC
2.50
wtsi-hgi
yggdrasil (https://github.com/wtsi-hgi/yggdrasil)
Node.js framework for hypr-based graph information systems
2.50
sanger-sequenceassembly
arcturus (https://github.com/sanger-sequenceassembly/arcturus)
Arcturus - a DNA sequence assembly management system
2.50
wtsi-npg
teepot (https://github.com/wtsi-npg/teepot)
2.38
sanger
lims-busclient (https://github.com/sanger/lims-busclient)
2.38
sanger
mixtio (https://github.com/sanger/mixtio)
2.38
sanger-pathogens
Bio-Pipeline-Comparison (https://github.com/sangerpathogens/Bio-Pipeline-Comparison)
2.38
sanger-pathogens
Bio-RetrieveAssemblies (https://github.com/sangerpathogens/Bio-RetrieveAssemblies)
2.38
sanger-pathogens
Bio-TypingGenerator (https://github.com/sangerpathogens/Bio-TypingGenerator)
2.38
sanger-pathogens
concordance (https://github.com/sangerpathogens/concordance)
2.38
sanger-pathogens
HICF_checklist (https://github.com/sangerpathogens/HICF_checklist)
2.38
VertebrateResequencing
update_pipeline (https://github.com/VertebrateResequencing/update_pipeline)
1.50
sanger
lims-api-examples (https://github.com/sanger/lims-apiexamples)
1.50
sanger
lims-quality-app (https://github.com/sanger/lims-quality-app)
1.50
sanger
mini-lims (https://github.com/sanger/mini-lims)
1.50
sanger-pathogens
Bio-GFFValidator (https://github.com/sanger-pathogens/BioGFFValidator)
1.50
sanger-pathogens
Bio-HICF-Schema (https://github.com/sanger-pathogens/BioHICF-Schema)
1.50
sanger-pathogens
Bio-HPS-FastTrack (https://github.com/sangerpathogens/Bio-HPS-FastTrack)
1.50
sanger-pathogens
Bio-Pequeno (https://github.com/sanger-pathogens/BioPequeno)
1.50
sanger-pathogens
Bio-Resistome (https://github.com/sanger-pathogens/BioResistome)
1.50
wtsi-hgi
update_pipeline (https://github.com/wtsi-hgi/update_pipeline)
1.50
wtsi-clarity
warehouse_messenger (https://github.com/wtsiclarity/warehouse_messenger)
A daemon that enhances messages from RabbitMQ and passes them on to a unified warehouse queue
1.00
Anacode
ensembl (https://github.com/Anacode/ensembl)
The Ensembl Core Perl API and SQL schema
1.00
Anacode
ensembl-pipeline (https://github.com/Anacode/ensemblpipeline)
Job management for the Ensembl Genebuild pipeline
1.00
Anacode
ensembl-test (https://github.com/Anacode/ensembl-test)
Test libraries and harnesses used for running the Ensembl test suite
1.00
Anacode
gff3_validator (https://github.com/Anacode/gff3_validator)
Online and command-line GFF3 validator
1.00
Anacode
git-yacontrib (https://github.com/Anacode/git-yacontrib)
Scripts I use on Git repositories
1.00
Anacode
HTtapTP (https://github.com/Anacode/HTtapTP)
TAP over HTTP
1.00
Anacode
HTTP-Async (https://github.com/Anacode/HTTP-Async)
Small hacks upon... process multiple HTTP requests in parallel without blocking
1.00
Anacode
perl-tk (https://github.com/Anacode/perl-tk)
perl-tk with local patch for BadWindow, and some tracing code on other branches.
1.00
Anacode
wikicloth (https://github.com/Anacode/wikicloth)
Ruby implementation of the MediaWiki markup language. In use for cvs2git-wrap/*.mediawiki as viewed through Github; bugfixes needed for ;term:def lists which I have used heavily.
1.00
wtsi-npg
bambamc (https://github.com/wtsi-npg/bambamc)
lightweight C implementation of name collating BAM file input and BAM file output
1.00
wtsi-npg
irods-legacy-gclp (https://github.com/wtsi-npg/irods-legacygclp)
This repository mirrors the legacy DICE-UCSD iRODS SVN repository at this time. No pull-requests will be merged back into trunk.
1.00
wtsi-npg
unveil (https://github.com/wtsi-npg/unveil)
A very lightweight jQuery plugin to lazy load images
1.00
VertebrateResequencing
vr-runner (https://github.com/VertebrateResequencing/vrrunner)
Runner pipelines
1.00
wtsi-medical-genomics
olorin (https://github.com/wtsi-medical-genomics/olorin)
Olorin is an interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees.
1.00
wtsi-medical-genomics
snoopy (https://github.com/wtsi-medical-genomics/snoopy)
Web-based quality control tool to review predicted variants in BAM files. Utilises the Dalliance genome browser.
1.00
wtsi-medical-genomics
snug (https://github.com/wtsi-medical-genomics/snug)
DNA sequencing QC application for rapidly viewing mapped reads at multiple sites from a SAM/BAM file
1.00
wtsi-medical-genomics
team-code (https://github.com/wtsi-medical-genomics/teamcode)
This repository aims to collect together any code that will aid team members in the course of their work.
1.00
sanger
barcode_warehouse (https://github.com/sanger/barcode_warehouse)
Simple barcode warehouse builder to assiste with reporting and later cross-lims barcode lookup
1.00
sanger
lims-exception-notifier-app (https://github.com/sanger/limsexception-notifier-app)
This application sends an e-mail if an exception has been raised in the host application.
1.00
sanger-pathogens
kraken (https://github.com/sanger-pathogens/kraken)
Kraken taxonomic sequence classification system
1.00
sanger-pathogens
structure (https://github.com/sanger-pathogens/structure)
Copy of Structure 2.3.4 with patch applied to fix seg fault
1.00
wtsi-hgi
13amp (https://github.com/wtsi-hgi/13amp)
Userspace CRAM-to-BAM translation virtual filesystem
1.00
wtsi-hgi
arvados (https://github.com/wtsi-hgi/arvados)
an open source platform for managing and analyzing biomedical big data
1.00
wtsi-hgi
bamboo (https://github.com/wtsi-hgi/bamboo)
HAProxy auto configuration and auto service discovery for Mesos Marathon
1.00
wtsi-hgi
baton (https://github.com/wtsi-hgi/baton)
iRODS client programs and API
1.00
wtsi-hgi
bcftools (https://github.com/wtsi-hgi/bcftools)
Human Genetics Informatics repository for bcftools (not official release)
1.00
wtsi-hgi
bcviz (https://github.com/wtsi-hgi/bcviz)
JavaScript visualisation for bamcheck file format
1.00
wtsi-hgi
beamer-scaffold (https://github.com/wtsi-hgi/beamer-scaffold)
Beamer presentation scaffold
1.00
wtsi-hgi
bhaps (https://github.com/wtsi-hgi/bhaps)
converters from text-based haplotype matrix to binary haplotype matrix, and for sampling haplotypes into genotypes
1.00
wtsi-hgi
bloch (https://github.com/wtsi-hgi/bloch)
BLOCH project
1.00
wtsi-hgi
chat-sharelatex (https://github.com/wtsi-hgi/chat-sharelatex)
The ShareLaTeX backend chat API
1.00
wtsi-hgi
clsi-sharelatex (https://github.com/wtsi-hgi/clsi-sharelatex)
A web api for compiling LaTeX documents in the cloud
1.00
wtsi-hgi
cvmfs (https://github.com/wtsi-hgi/cvmfs)
The CernVM File System
1.00
wtsi-hgi
cvmfs-test (https://github.com/wtsi-hgi/cvmfs-test)
A test framework for the CernVM-FS
1.00
wtsi-hgi
DNAOrderApp (https://github.com/wtsi-hgi/DNAOrderApp)
Refining the process for ordering DNA Sequences
1.00
wtsi-hgi
docker-texlive (https://github.com/wtsi-hgi/docker-texlive)
Dockerfile to build a trusted build of a container including texlive
1.00
wtsi-hgi
docker-ubuntu-python-pip (https://github.com/wtsi-hgi/dockerubuntu-python-pip)
Trusted docker build based on ubuntu with addition of Python and pip
1.00
wtsi-hgi
docstore-sharelatex (https://github.com/wtsi-hgi/docstoresharelatex)
A CRUD API for storing and updating text documents in projects
1.00
wtsi-hgi
document-updater-sharelatex (https://github.com/wtsihgi/document-updater-sharelatex)
An API for applying incoming updates to documents in real-time
1.00
wtsi-hgi
dstat (https://github.com/wtsi-hgi/dstat)
Versatile resource statistics tool
1.00
wtsi-hgi
ep_doi (https://github.com/wtsi-hgi/ep_doi)
Etherpad Lite plugin to enable doi: identifiers (linking automatically to http://dx.doi.org/)
1.00
wtsi-hgi
ep_html_export_using_client_filters (https://github.com/wtsihgi/ep_html_export_using_client_filters)
Etherpad Lite plugin to allow use of client-side filters for HTML export (generates messier HTML, but allows plugins like ep_doi and ep_pubmed to work for HTML export)
1.00
wtsi-hgi
etherpad-lite (https://github.com/wtsi-hgi/etherpad-lite)
An Etherpad based on node.js - Our goal is to make collaborative editing the standard on the web
1.00
wtsi-hgi
filestore-sharelatex (https://github.com/wtsi-hgi/filestoresharelatex)
An API for CRUD operations on binary files stored in S3
1.00
wtsi-hgi
flask (https://github.com/wtsi-hgi/flask)
A microframework based on Werkzeug, Jinja2 and good intentions (unofficial fork)
1.00
wtsi-hgi
flask-restful (https://github.com/wtsi-hgi/flask-restful)
Simple framework for creating REST APIs (unofficial fork)
1.00
wtsi-hgi
freebayes (https://github.com/wtsi-hgi/freebayes)
Bayesian haplotype-based polymorphism discovery and genotyping.
1.00
wtsi-hgi
gatk-protected (https://github.com/wtsi-hgi/gatk-protected)
GATK Official Release Repository: contains the core MIT-licensed GATK framework, plus "protected" tools restricted to noncommercial use only
1.00
wtsi-hgi
GEMMA (https://github.com/wtsi-hgi/GEMMA)
Genome-wide Efficient Mixed Model Association
1.00
wtsi-hgi
graph (https://github.com/wtsi-hgi/graph)
Graph package providing various implementations of graph data structures and graph processing algorithms.
1.00
wtsi-hgi
hapi-ur (https://github.com/wtsi-hgi/hapi-ur)
HAPI-UR: HAPlotype Inference for UnRelated samples (cloned from: https://code.google.com/p/hapi-ur)
1.00
wtsi-hgi
hattie (https://github.com/wtsi-hgi/hattie)
Control panel for HGI Users to Request work be done
1.00
wtsi-hgi
henplus (https://github.com/wtsi-hgi/henplus)
HenPlus is a SQL shell that can handle multiple sessions in parallel. The commandline interface with the usual history functions features TAB-completion for commands, tables and columns. Database connect via JDBC.
1.00
wtsi-hgi
hgc-deploy (https://github.com/wtsi-hgi/hgc-deploy)
Tools for creating and running Mercury containers. (now deprecated in favour of hgc-tools)
1.00
wtsi-hgi
hgc-tools (https://github.com/wtsi-hgi/hgc-tools)
Set of tools for working with Mercury capsules.
1.00
wtsi-hgi
hgi-bamcheck-server (https://github.com/wtsi-hgi/hgibamcheck-server)
Serves bamcheck files from vrpipe via http
1.00
wtsi-hgi
hgi-qc-frontend (https://github.com/wtsi-hgi/hgi-qc-frontend)
Web frontend for qc data
1.00
wtsi-hgi
hgi-reports (https://github.com/wtsi-hgi/hgi-reports)
Various reports for compute and storage usage.
1.00
wtsi-hgi
hgi-rt (https://github.com/wtsi-hgi/hgi-rt)
RT customisations for HGI
1.00
wtsi-hgi
hgi-vrtrack-qc-server (https://github.com/wtsi-hgi/hgi-vrtrackqc-server)
Serves QC data from vrtrack database via http.
1.00
wtsi-hgi
hgi-web_apitoken (https://github.com/wtsi-hgi/hgiweb_apitoken)
Issue API access tokens to otherwise authenticated clients
1.00
wtsi-hgi
hgi-web_usermod (https://github.com/wtsi-hgi/hgiweb_usermod)
User roles authentication module for HGI-web
1.00
wtsi-hgi
hts-specs (https://github.com/wtsi-hgi/hts-specs)
SAM/BAM specification
1.00
wtsi-hgi
htslib (https://github.com/wtsi-hgi/htslib)
C library for high-throughput sequencing data formats
1.00
wtsi-hgi
illumina2bam (https://github.com/wtsi-hgi/illumina2bam)
Generate and process BAM files from Illumina sequencing instrument files
1.00
wtsi-hgi
iquestFuse (https://github.com/wtsi-hgi/iquestFuse)
iquest-like iRODS FUSE client (allows navigation of metadata via a virtual POSIX filesystem)
1.00
wtsi-hgi
irods (https://github.com/wtsi-hgi/irods)
Middleware for your critical data.
1.00
wtsi-hgi
iRODS-Solr (https://github.com/wtsi-hgi/iRODS-Solr)
Offload irods metadata querying to an apache solr instance
1.00
wtsi-hgi
IYG-Import (https://github.com/wtsi-hgi/IYG-Import)
Python Data Importer for IYG Web
1.00
wtsi-hgi
IYG-SOT-Web (https://github.com/wtsi-hgi/IYG-SOT-Web)
SNP and Trait description crowdsourcing site for the Inside Your Genome project.
1.00
wtsi-hgi
IYG-SOT-Web-Lib (https://github.com/wtsi-hgi/IYG-SOT-WebLib)
Inside Your Genome Trait and SNP description Crowdsourcing Site Perl Modules
1.00
wtsi-hgi
IYG-Web (https://github.com/wtsi-hgi/IYG-Web)
"Inside Your Genome" Web App
1.00
wtsi-hgi
IYG-Web-Lib (https://github.com/wtsi-hgi/IYG-Web-Lib)
Perl Library for IYG Web
1.00
9.89
9.60
9.27
8.64
7.51
6.26
5.87
5.72
Modularised versions of *find scripts
wtsi-hgi
jquery-dynatable (https://github.com/wtsi-hgi/jquerydynatable)
A more-fun, semantic, alternative to datatables
1.00
wtsi-hgi
jsql (https://github.com/wtsi-hgi/jsql)
Java program to allow connecting to any database to run select queries, and outputting the results in various formats. Mainly used to return data from sql queries in a form that can be easily eval'd in python.
1.00
wtsi-hgi
kaiwa (https://github.com/wtsi-hgi/kaiwa)
A modern XMPP Web client
1.00
wtsi-hgi
logger-sharelatex (https://github.com/wtsi-hgi/loggersharelatex)
A module encapsulating standard logging features for ShareLaTeX services
1.00
wtsi-hgi
lustre_changelog_dummy (https://github.com/wtsihgi/lustre_changelog_dummy)
Dummy program to test lustre changelogs
1.00
wtsi-hgi
lustre_operator (https://github.com/wtsi-hgi/lustre_operator)
Wrapper script to allow non-root users to run privileged lfs commands on particular Lustre filesystems (using sudo)
1.00
wtsi-hgi
metadata-check (https://github.com/wtsi-hgi/metadata-check)
Tests to perform on the iRODS metadata for a BAM file, versus the information in the file header
1.00
wtsi-hgi
metrics-sharelatex (https://github.com/wtsi-hgi/metricssharelatex)
A drop-in metrics and monitoring module for node.js apps
1.00
wtsi-hgi
mkfs_udf_portable_hd (https://github.com/wtsihgi/mkfs_udf_portable_hd)
Perl utility to format UDF hard drive on Linux for portable use across Linux, Mac, and Windows
1.00
wtsi-hgi
mod-proxy-add-user (https://github.com/wtsi-hgi/mod-proxyadd-user)
a tiny apache module to pass REMOTE_USER via headers to proxy servers
1.00
wtsi-hgi
modules (https://github.com/wtsi-hgi/modules)
Fork of http://modules.sourceforge.net/ (this version has been modified primarily to add more complete bash completion as well as tcsh completion)
1.00
wtsi-hgi
mpistat (https://github.com/wtsi-hgi/mpistat)
Efficiently lstat every file in a filesystem tree in parallel across multiple nodes using MPI.
1.00
wtsi-hgi
node-http-write (https://github.com/wtsi-hgi/node-http-write)
Raw HTTP response writer with basic templating
1.00
wtsi-hgi
pcp (https://github.com/wtsi-hgi/pcp)
Parallel copy tool
1.00
wtsi-hgi
petardfs (https://github.com/wtsi-hgi/petardfs)
PetardFS - a FUSE filessytem for injecting intentional errors (e.g. for testing)
1.00
wtsi-hgi
Platypus (https://github.com/wtsi-hgi/Platypus)
Platypus Variant Caller
1.00
wtsi-hgi
profiles (https://github.com/wtsi-hgi/profiles)
contributed profiles
1.00
wtsi-hgi
proxygen (https://github.com/wtsi-hgi/proxygen)
A collection of C++ HTTP libraries including an easy to use HTTP server.
1.00
wtsi-hgi
python-rt (https://github.com/wtsi-hgi/python-rt)
Clone of git://git.nic.cz/python-rt.git
1.00
wtsi-hgi
r-travis (https://github.com/wtsi-hgi/r-travis)
Tools for using R with Travis (http://travis-ci.org)
1.00
wtsi-hgi
redis-sharelatex (https://github.com/wtsi-hgi/redis-sharelatex)
a wrapper around redis which detects if it should use the normal redis driver or redis-sentinel
1.00
wtsi-hgi
rendr (https://github.com/wtsi-hgi/rendr)
Render your Backbone.js apps on the client and the server, using Node.js.
1.00
wtsi-hgi
replace_reads (https://github.com/wtsi-hgi/replace_reads)
Replaces reads in a BAM file
1.00
wtsi-hgi
rt-integration (https://github.com/wtsi-hgi/rt-integration)
Fetches tickets from RT (using REST API) and sends them to webhook
1.00
wtsi-hgi
rt-subject-from-fields (https://github.com/wtsi-hgi/rt-subjectfrom-fields)
Set subject of RT tickets based on field values (including custom fields)
1.00
wtsi-hgi
samtools (https://github.com/wtsi-hgi/samtools)
Human Genetics Informatics repository for samtools (not official release)
1.00
wtsi-hgi
serf (https://github.com/wtsi-hgi/serf)
Service orchestration and management tool.
1.00
wtsi-hgi
settings-sharelatex (https://github.com/wtsi-hgi/settingssharelatex)
A small module to allow global config settings to be set for all services within the ShareLaTeX architecture.
1.00
wtsi-hgi
spec (https://github.com/wtsi-hgi/spec)
ALPS Specification documents.
1.00
wtsi-hgi
spelling-sharelatex (https://github.com/wtsi-hgi/spellingsharelatex)
The backend spellcheck API that performs spell checking for ShareLaTeX
1.00
wtsi-hgi
supervisor (https://github.com/wtsi-hgi/supervisor)
Supervisor process control system for UNIX
1.00
wtsi-hgi
tabix (https://github.com/wtsi-hgi/tabix)
Note: tabix and bgzip binaries are now part of the HTSlib project.
1.00
wtsi-hgi
tags-sharelatex (https://github.com/wtsi-hgi/tags-sharelatex)
An API for managing project tags/folders in ShareLaTeX
1.00
wtsi-hgi
track-changes-sharelatex (https://github.com/wtsi-hgi/trackchanges-sharelatex)
An API for saving and compressing individual document updates into a browsable history
1.00
wtsi-hgi
translations-sharelatex (https://github.com/wtsihgi/translations-sharelatex)
holds the translations used for ShareLaTeX.com
1.00
wtsi-hgi
triple-e (https://github.com/wtsi-hgi/triple-e)
Docker and Boot2Docker wrapper scripts
1.00
wtsi-hgi
vcftools (https://github.com/wtsi-hgi/vcftools)
Mirror of SVN from http://svn.code.sf.net/p/vcftools/code/
1.00
wtsi-hgi
vg (https://github.com/wtsi-hgi/vg)
tools for working with variant graphs
1.00
wtsi-hgi
vr-codebase (https://github.com/wtsi-hgi/vr-codebase)
The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute (HGI edition)
1.00
wtsi-hgi
vr-pipe (https://github.com/wtsi-hgi/vr-pipe)
Generic pipeline system
1.00
wtsi-hgi
web-sharelatex (https://github.com/wtsi-hgi/web-sharelatex)
The web front end for ShareLaTeX, a web-based collaborative LaTeX editor
1.00
wtsi-hgi
werkzeug (https://github.com/wtsi-hgi/werkzeug)
A flexible WSGI implementation and toolkit (unofficial fork)
1.00
wtsi-hgi
wings (https://github.com/wtsi-hgi/wings)
WINGS Workflow System
1.00
wtsi-hgi
xiongxiong (https://github.com/wtsi-hgi/xiongxiong)
Bearer token codec
1.00
wtsi-hgi
XKCD-password-generator (https://github.com/wtsihgi/XKCD-password-generator)
Generate secure multiword passwords/passphrases, inspired by XKCD
1.00
samtools
glftools (https://github.com/samtools/glftools)
0.00
wtsi-web
pagesmith-core (https://github.com/wtsi-web/pagesmith-core)
0.00
wtsi-web
pagesmith-oa2-provider (https://github.com/wtsiweb/pagesmith-oa2-provider)
0.00
wtsi-ssg
objectbench (https://github.com/wtsi-ssg/objectbench)
0.00
sanger
lims-history-app (https://github.com/sanger/lims-history-app)
0.00
sanger
uuid_service (https://github.com/sanger/uuid_service)
0.00
sanger-pathogens
annotations_update (https://github.com/sangerpathogens/annotations_update)
0.00
wtsi-hgi
dockerfile-arangodb (https://github.com/wtsi-hgi/dockerfilearangodb)
0.00
wtsi-hgi
hgi-bamcheck-frontend (https://github.com/wtsi-hgi/hgibamcheck-frontend)
0.00
wtsi-hgi
hgi-scripts (https://github.com/wtsi-hgi/hgi-scripts)
0.00
wtsi-hgi
serapis-web (https://github.com/wtsi-hgi/serapis-web)
0.00
wtsi-hgi
tarchecksum (https://github.com/wtsi-hgi/tarchecksum)
0.00
wtsi-hgi
translate_header (https://github.com/wtsihgi/translate_header)
0.00
wtsi-hgi
treeserve (https://github.com/wtsi-hgi/treeserve)
0.00
Data collected: 2015-08-14 20:02:32