- The McDonnell Genome Institute
33 14A tool to call somatic single nucleotide variants.
12 2iBWA is a fork of Heng Li's BWA aligner with support for iteratively adding alternate haplotypes, reference patches, and variant hypotheses.
2 1An approximate sequence pattern matcher for FASTQ/FASTA files.
2 0extract 454 Genome Sequencer reads from a SFF file and convert them into a FASTQ formatted output
0 1A fork of chimerascan that supports variable read lengths
122 84Pindel 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.
86 41SV detection from paired end reads mapping
22 12a tool for processing .bed and .vcf files
2 2simple static plots of read pairing information
1 2A fork of dindel
0 0A tool to examine duplicate read characteristics in a BAM file
Common Workflow Language
68 33Open workflow definitions for genomic analysis from MGI at WUSM.
26 17MGI's CWL Cancer Pipelines.
2 2Docker container for the star aligner
0 4Docker container for bcftools
0 3a fat pipeline for running WGBS analysis
0 1docker image for running duphold
0 0fork of the quay.io homer image, moving annotations to my hardcoded link
0 0Docker cotainer for mixcr t/b-cell toolkit
0 0Jekyll site for Genome Modeling Tools
11 9Analyze exome data for Mendelian disorders. Still in alpha-testing.
1 3Website for Variant Interpretation for Cancer Consortium:
70 24The Genome Modeling System installer
44 56Core modules used by the GMS
3 13Rich Transactional Objects for Perl
3 1scripts and modules to facilitate comparing gold standard VCFs
2 4Washington University Genome Center Hudson testing suite and deploy scripts
1 4the workflow server used at TGI
0 1Repo for cle myeloseq/haloplex assay
0 9Docker containerization for the CLE
0 5Perl interface to the PTero services
0 1Commands and Modules used by the Reference Improvement group.
0 0RefImp Scripts and Code that are Dependent on the LIMS Code and DB
0 4Provide access to various genome services such as procera, amber, and others.
0 0CLI to Manage and Store 10X Genomics Objects
0 3RESTful service to manage ephemeral PostgreSQL databases
0 6Mirror of internal repository for TestTracker.
3 1Graphite Config and Cron Scripts
160 61count DNA sequence reads in BAM files
5 0This is a python command line client for Atlassian's Jira issue tracker.
4 3Create JIRA issues when keywords are matched in RSS feeds.
4 9Supplementary data for Petti, et al 2019 scRNA mutation publication
1 1common build scripts used in c/c++ projects
1 5Ptero services to run commands via LSF
1 5Petri net core of the PTero system
1 6Client-facing API for the PTero system
0 0Docker image for running xenosplit
0 3A simplified interface to LSF built on top of existing C bindings.
0 0A command line interface for the Nessy locking service.
77 44An R package for inferring the subclonal architecture of tumors
6 12accessory scripts and documentation related to the sciclone R package at genome/sciclone
3 8R package that uses a variational Bayesian approach to fitting a mixture of Beta distributions
3 10A fat docker image for running RnaSeq
0 0R Shiny code for comparing user-uploaded SNVs with those derived from ultra-deep sequencing
0 1in-progress port of our webviews to rails
0 0Scripts for generating the GMT site from public GitHub repos
0 1Biscuit + htslib for bgzip
0 1Repo for cle related software