genome

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docs

 22  0

tigra-sv

 8  2

cncwl

 1  0

docker-fgbio

 1  1
A docker image for using fgbio

docker-gossamer

 1  1
Docker container for gossamer bioinformatics suite

docker-strelka

 1  3
A docker image for Strelka

docker-vep-cwl

 1  2
Variant of vep image without an ENTRYPOINT

somatic-snv-test-data

 1  0
Example Data for SomaticSniper

docker-bam-readcount

 0  3
Docker containerization for "bam-readcount"

docker-bam-readcount-cwl

 0  1

docker-expansionhunter

 0  1
Docker image for running https://github.com/Illumina/ExpansionHunter

docker-fpfilter

 0  1
Docker container for false positive filter

docker-fpfilter-cwl

 0  1
version of docker-fpfilter without an entrypoint

docker-interval_list_tools-cwl

 0  1
A Docker image for Picard IntervalListTools with helper scripts.

docker-pindel

 0  1
Docker container for pindel

docker-pindel2vcf

 0  1
pindel2vcf docker container

docker-pindel-cwl

 0  1
pindel docker container for cwl

docker-pindelsomaticfilter

 0  1
pindelsomaticfilter docker container

docker-pindelsomaticfilter-cwl

 0  1
pindelsomaticfilter docker container for cwl

docker-samtools

 0  2
Docker container for Samtools

docker-strelka-cwl

 0  3
A wrapper for the docker-strelka image for use in CWL-based workflows.

docker-stretch

 0  1
Docker image for https://github.com/Oshlack/STRetch

docker-tabix

 0  2
Docker entrypoint for tabix

docker-tabix-cwl

 0  2
Variant of the mgibio/tabix image without an ENTRYPOINT.

docker-varscan

 0  2
A docker image for Varscan

docker-varscan-cwl

 0  3
Combination varscan/samtools container for easier running in workflows.

docker-vep

 0  3
Docker containerization for Ensembl Variant Effect Predictor

ptero-apis

 0  3
Design documents for the PTero services
C

somatic-sniper

 37  16
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

 134  87
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

 88  43
SV detection from paired end reads mapping

joinx

 22  11
a tool for processing .bed and .vcf files

dindel-tgi

 3  1
A fork of dindel

pairoscope

 2  3
simple static plots of read pairing information
Common Workflow Language

analysis-workflows

 81  46
Open workflow definitions for genomic analysis from MGI at WUSM.
Dockerfile

docker-star

 3  3
Docker container for the star aligner

docker-samtools-cwl

 1  0

docker-alignment_helper-cwl

 0  3

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-checkstrandedness

 0  1

docker-cnvkit

 0  1

docker-duphold

 0  1
docker image for running duphold

docker-fp_filter-cwl

 0  2
This is the one used in current CWL pipelines - pulls from fpfilter-tool

docker-gatk-cwl

 0  1

docker-gdc-client

 0  1
docker image for running the gdc client

docker-manta_somatic-cwl

 0  1

docker-mark_duplicates-cwl

 0  1

docker-multiqc

 0  1
dockerization of multiqc

docker-sambamba-cwl

 0  1

docker-SURVIVOR-cwl

 0  1
Go

log2file

 0  1
HTML

bfx-workshop

 17  7
Java

mendelscan

 11  8
Analyze exome data for Mendelian disorders. Still in alpha-testing.
JavaScript

flow-core

 2  2

ptero-workflow-client

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

genome-sqitch

 0  3
Perl

gms

 70  24
The Genome Modeling System installer

genome

 55  57
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  5
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

docker-basespace_chromoseq

 0  5

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-vep_helper-cwl

 0  3

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.

rex

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

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

ptero-puppet

 0  3
Python

bam-readcount

 182  71
count DNA sequence reads in BAM files

scrna_mutations

 6  11
Supplementary data for Petti, et al 2019 scRNA mutation publication

jiraclient

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

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

cle-chromoseq

 1  4
Repository for CLE ChromoSeq Assay

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-mapq0-filter

 0  1
filter a vcf for variants with high percentage of mapq0 reads

docker-somatic-llr-filter

 0  2
Container for the somatic-llr filter

flow-examples

 0  1

flow-workflow

 0  2

lsf-python

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

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
R

sciclone

 91  47
An R package for inferring the subclonal architecture of tumors

sciclone-meta

 6  12
accessory scripts and documentation related to the sciclone R package at genome/sciclone

docker-rnaseq

 4  10
A fat docker image for running RnaSeq

bmm

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

aml31Benchmarking

 2  0
Ruby

gms-webviews

 0  1
in-progress port of our webviews to rails

mcollective-users-agent

 0  1
Examine active users with this mcollective RPC agent.

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  2
Biscuit + htslib for bgzip

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
wdl

qc-analysis-pipeline

 2  3
Workflow used for WGS/WES data QC

cle

 1  1
Repo for cle related software

dockstore-workflow-index-reference

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