The McDonnell Genome Institute http://genome.wustl.edu/ 171 1,206 814 No Language docs 22 0 tigra-sv 8 2 cncwl 1 0 docker-fgbio 1 1 A docker image for using fgbio docker-gossamer 1 0 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 1 Example Data for SomaticSniper 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 40 16 A tool to call somatic single nucleotide variants. ibwa 13 2 iBWA is a fork of Heng Li's BWA aligner with support for iteratively adding alternate haplotypes, reference patches, and variant hypotheses. fqgrep 3 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 160 90 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 110 44 SV detection from paired end reads mapping joinx 21 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 CMake bam-readcount 295 95 Count bases in BAM/CRAM files Common Workflow Language analysis-workflows 102 58 Open workflow definitions for genomic analysis from MGI at WUSM. Dockerfile docker-star 3 6 Docker container for the star aligner docker-bcftools 2 5 Docker container for bcftools docker-samtools-cwl 1 2 docker-alignment_helper-cwl 0 3 docker-annotsv-cwl 0 5 Docker container for running AnnotSV docker-bam-readcount 0 4 Docker containerization for "bam-readcount" 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 3 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-homer 0 2 fork of the quay.io homer image, moving annotations to my hardcoded link 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 47 19 Java mendelscan 10 7 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 77 23 The Genome Modeling System installer genome 64 57 Core modules used by the GMS fpfilter-tool 6 9 UR 4 12 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 cle-myeloseq 1 1 Repo for cle myeloseq/haloplex assay 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 docker-basespace_chromoseq 0 4 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. Perl 6 graphite 3 1 Graphite Config and Cron Scripts Puppet ptero-puppet 0 3 Python scrna_mutations 16 13 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 5 3 Create JIRA issues when keywords are matched in RSS feeds. AGFusion 4 5 Python package to annotate and visualize gene fusions. docker-bam_readcount_helper-cwl 3 10 cle-myeloseqhd 2 4 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 2 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 2 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 112 55 An R package for inferring the subclonal architecture of tumors sciclone-meta 6 15 accessory scripts and documentation related to the sciclone R package at genome/sciclone bmm 4 9 R package that uses a variational Bayesian approach to fitting a mixture of Beta distributions docker-rnaseq 4 10 A fat docker image for running RnaSeq 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 docker-dna-alignment 2 3 A fat docker image for running alignment cancer-genomics-workflow-wiki 1 3 A full featured, including pull requests, git repo for the arvados_trial Wiki 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 6 7 Workflow used for WGS/WES data QC wdl 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.
