genome

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C

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
A fork of chimerascan that supports variable read lengths

C++

pindel

122 84
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

86 41
SV detection from paired end reads mapping

joinx

22 12
a tool for processing .bed and .vcf files
simple static plots of read pairing information
A fork of dindel
A tool to examine duplicate read characteristics in a BAM file

Common Workflow Language

Open workflow definitions for genomic analysis from MGI at WUSM.
MGI's CWL Cancer Pipelines.

Dockerfile

Docker container for the star aligner
Docker container for running AnnotSV
Docker container for bcftools
Variant of bcftools image without an ENTRYPOINT
a fat pipeline for running WGBS analysis
docker image for running duphold
This is the one used in current CWL pipelines - pulls from fpfilter-tool
fork of the quay.io homer image, moving annotations to my hardcoded link
Docker cotainer for mixcr t/b-cell toolkit

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

Website for Variant Interpretation for Cancer Consortium:

vicc

1 3
Website for Variant Interpretation for Cancer Consortium:

flow-core

0 1
This is a web client for the PTero workflow service

PLpgSQL

Perl

gms

70 24
The Genome Modeling System installer

genome

44 56
Core modules used by the GMS

UR

3 13
Rich Transactional Objects for Perl
scripts and modules to facilitate comparing gold standard VCFs
Washington University Genome Center Hudson testing suite and deploy scripts
custom tab−completion for Perl apps
Perl client for the nessy-server lock daemon
the workflow server used at TGI
Repo for cle myeloseq/haloplex assay
Autoloading configuration manager for use in the genome modeling system
Docker containerization for the CLE
Repo for several report scripts used for cle aml trio cwl
Docker for Running Sqitch with MySQL on Trusty at MGI

procera

0 4
Perl interface to the PTero services

refimp

0 1
Commands and Modules used by the Reference Improvement group.
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
RESTful service to manage ephemeral PostgreSQL databases
Mirror of internal repository for TestTracker.
Create/Read/Update/Delete Command classes for UR objects

Perl 6

graphite

3 1
Graphite Config and Cron Scripts

Puppet

Python

bam-readcount

160 61
count DNA sequence reads in BAM files
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.
Supplementary data for Petti, et al 2019 scRNA mutation publication
common build scripts used in c/c++ projects

ptero-lsf

1 5
Ptero services to run commands via LSF
Petri net core of the PTero system
Client-facing API for the PTero system
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
Docker containerization of tools needed for concordance tool
Container for the somatic-llr filter
Docker image for running xenosplit
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 services to run shell commands
A pre-workflow script to stage cwl workflow inputs in a single directory

R

sciclone

77 44
An R package for inferring the subclonal architecture of tumors
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
A fat docker image for running RnaSeq
docker image seurat
R Shiny code for comparing user-uploaded SNVs with those derived from ultra-deep sequencing

Ruby

in-progress port of our webviews to rails
Scripts for generating the GMT site from public GitHub repos
Examine active users with this mcollective RPC agent.
Puppet module for managing PostgreSQL

spectacle

0 2

Shell

ptero

9 4
A full featured, including pull requests, git repo for the arvados_trial Wiki
A fat docker image for running alignment
Biscuit + htslib for bgzip
filter a vcf for variants with high percentage of mapq0 reads
Barebones debian files to make a passenger deb.
DO NOT USE !! meta package for installing genome dependencies

wdl

cle

0 1
Repo for cle related software
A dockstore compatible workflow repository for indexing a reference genome sequence.
Workflow used for WGS data QC