genome

C

somatic-sniper

34 14
A tool to call somatic single nucleotide variants.

ibwa

12 2
iBWA is a fork of Heng Li's BWA aligner with support for iteratively adding alternate haplotypes, reference patches, and variant hypotheses.

fqgrep

2 1
An approximate sequence pattern matcher for FASTQ/FASTA files.

sff2fastq

2 0
extract 454 Genome Sequencer reads from a SFF file and convert them into a FASTQ formatted output

chimerascan-vrl

0 1
A fork of chimerascan that supports variable read lengths

C++

pindel

126 85
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

breakdancer

87 43
SV detection from paired end reads mapping

joinx

22 12
a tool for processing .bed and .vcf files

dindel-tgi

2 2
A fork of dindel

pairoscope

2 2
simple static plots of read pairing information

diagnose_dups

0 0
A tool to examine duplicate read characteristics in a BAM file

Common Workflow Language

analysis-workflows

71 38
Open workflow definitions for genomic analysis from MGI at WUSM.

cancer-genomics-workflow

26 17
MGI's CWL Cancer Pipelines.

Dockerfile

docker-star

2 2
Docker container for the star aligner

docker-samtools-cwl

1 0

docker-alignment_helper-cwl

0 2

docker-annotsv-cwl

0 1
Docker container for running AnnotSV

docker-bcftools

0 4
Docker container for bcftools

docker-bcftools-cwl

0 3
Variant of bcftools image without an ENTRYPOINT

docker-bisulfite

0 3
a fat pipeline for running WGBS analysis

docker-cnvkit

0 1

docker-cnvnator-cwl

0 0

docker-data_downloader

0 0

docker-duphold

0 1
docker image for running duphold

docker-fp_filter-cwl

0 1
This is the one used in current CWL pipelines - pulls from fpfilter-tool

docker-gatk-cwl

0 1

docker-grolar-cwl

0 0

docker-homer

0 0
fork of the quay.io homer image, moving annotations to my hardcoded link

docker-immuno_tools-cwl

0 0

docker-manta_somatic-cwl

0 0

docker-mark_duplicates-cwl

0 1

docker-mixcr

0 0
Docker cotainer for mixcr t/b-cell toolkit

docker-picard-cwl

0 0

docker-pizzly-cwl

0 0

docker-sambamba-cwl

0 1

docker-SURVIVOR-cwl

0 1

docker-vcf_annotation_tools-cwl

0 1

docker-verify_bam_id-cwl

0 0

Go

log2file

0 1

HTML

gmt-site

0 0
Jekyll site for Genome Modeling Tools

Java

mendelscan

11 9
Analyze exome data for Mendelian disorders. Still in alpha-testing.

JavaScript

cancervariants.org

2 4
Website for Variant Interpretation for Cancer Consortium:

flow-core

1 1

vicc

1 3
Website for Variant Interpretation for Cancer Consortium:

ptero-workflow-client

0 2
This is a web client for the PTero workflow service

PLpgSQL

genome-sqitch

0 3

Perl

gms

71 24
The Genome Modeling System installer

genome

49 55
Core modules used by the GMS

fpfilter-tool

6 6

UR

3 13
Rich Transactional Objects for Perl

vcf-evaluation

3 1
scripts and modules to facilitate comparing gold standard VCFs

tgi-workflow

2 4
the workflow server used at TGI

wugc-hudson

2 4
Washington University Genome Center Hudson testing suite and deploy scripts

Getopt--Complete-for-Perl

1 2
custom tab−completion for Perl apps

nessy-client-perl

1 2
Perl client for the nessy-server lock daemon

cle-myeloseq

0 1
Repo for cle myeloseq/haloplex assay

configuration-manager

0 0
Autoloading configuration manager for use in the genome modeling system

docker-basespace_chromoseq

0 1

docker-cle

0 9
Docker containerization for the CLE

docker-cle-aml-trio-reports

0 1
Repo for several report scripts used for cle aml trio cwl

docker-perl_helper-cwl

0 1

docker-sqitch-mysql

0 0
Docker for Running Sqitch with MySQL on Trusty at MGI

docker-vep_helper-cwl

0 2

procera

0 4

ptero-perl-sdk

0 5
Perl interface to the PTero services

refimp

0 1
Commands and Modules used by the Reference Improvement group.

refimp-lims

0 0
RefImp Scripts and Code that are Dependent on the LIMS Code and DB

rex

0 4
Provide access to various genome services such as procera, amber, and others.

tenx

0 0
CLI to Manage and Store 10X Genomics Objects

TestDbServer

0 3
RESTful service to manage ephemeral PostgreSQL databases

TestTracker

0 6
Mirror of internal repository for TestTracker.

UR-Object-Command-Crud

0 1
Create/Read/Update/Delete Command classes for UR objects

Perl 6

graphite

3 1
Graphite Config and Cron Scripts

Puppet

nnutter-perlbrew

0 0

nnutter-testdb

0 0

ptero-puppet

0 3

Python

bam-readcount

163 61
count DNA sequence reads in BAM files

jiraclient

5 0
This is a python command line client for Atlassian's Jira issue tracker.

scrna_mutations

5 9
Supplementary data for Petti, et al 2019 scRNA mutation publication

rss2jira

4 3
Create JIRA issues when keywords are matched in RSS feeds.

docker-bam_readcount_helper-cwl

3 10

ptero-lsf

2 5
Ptero services to run commands via LSF

build-common

1 1
common build scripts used in c/c++ projects

docker-custom-clinvar-vcf

1 0

nessy-server

1 1

ptero-petri

1 6
Petri net core of the PTero system

ptero-workflow

1 6
Client-facing API for the PTero system

qc-metric-aggregator

1 0
Given the output directory of a QC pipeline and a threshold config file, parse out the desired metrics and evalute them against the thresholds.

amber

0 3

concordance

0 1

docker-annotation_table-cwl

0 1

docker-concordance

0 0
Docker containerization of tools needed for concordance tool

docker-copynum

0 0

docker-depth-filter

0 0

docker-somatic-llr-filter

0 2
Container for the somatic-llr filter

docker-xenosplit

0 0
Docker image for running xenosplit

flow-examples

0 1

flow-workflow

0 2

lsf-python

0 3
A simplified interface to LSF built on top of existing C bindings.

nessy-cli

0 0
A command line interface for the Nessy locking service.

ptero-auth

0 3

ptero-benchmarking

0 3

ptero-common

0 3

ptero-deployment

0 3

ptero-shell-command

0 4
Ptero services to run shell commands

standalone-input-staging

0 0
A pre-workflow script to stage cwl workflow inputs in a single directory

R

sciclone

80 43
An R package for inferring the subclonal architecture of tumors

sciclone-meta

6 11
accessory scripts and documentation related to the sciclone R package at genome/sciclone

bmm

3 8
R package that uses a variational Bayesian approach to fitting a mixture of Beta distributions

docker-rnaseq

3 10
A fat docker image for running RnaSeq

aml31Benchmarking

2 0

docker-scrna_lineage_inference

0 0
docker image seurat

shiny_aml31

0 0
R Shiny code for comparing user-uploaded SNVs with those derived from ultra-deep sequencing

Ruby

gms-webviews

0 1
in-progress port of our webviews to rails

gmt-site-builder

0 0
Scripts for generating the GMT site from public GitHub repos

mcollective-users-agent

0 1
Examine active users with this mcollective RPC agent.

puppetlabs-postgresql

0 0
Puppet module for managing PostgreSQL

spectacle

0 2

Shell

ptero

9 4

cancer-genomics-workflow-wiki

1 3
A full featured, including pull requests, git repo for the arvados_trial Wiki

docker-dna-alignment

1 4
A fat docker image for running alignment

docker-biscuit

0 1
Biscuit + htslib for bgzip

docker-mapq0-filter

0 0
filter a vcf for variants with high percentage of mapq0 reads

docker-varscan_helper-cwl

0 0

genome_rails_prod

0 1
Barebones debian files to make a passenger deb.

genome-snapshot-deps

0 8
DO NOT USE !! meta package for installing genome dependencies

git-gerrit

0 0

wdl

qc-analysis-pipeline

1 2
Workflow used for WGS data QC

cle

0 1
Repo for cle related software

dockstore-workflow-index-reference

0 1
A dockstore compatible workflow repository for indexing a reference genome sequence.