Alternatives and similar repositories for cromshell:

Users that are interested in cromshell are comparing it to the libraries listed below

• broadinstitute / cromwell-tools
  A collection of Python clients and accessory scripts for interacting with the Cromwell
  ☆22Updated 2 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆67Updated 4 months ago
• svviz / svviz
  Read visualizer for structural variants
  ☆81Updated 6 years ago
• CCDG / Pipeline-Standardization
  ☆82Updated 6 years ago
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆37Updated 3 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆96Updated 2 years ago
• vplagnol / ExomeDepth
  ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
  ☆69Updated last year
• ga4gh / quality-control-wgs
  Home for the GA4GH Quality Control of Whole Genome Sequencing metrics and reference implementations
  ☆14Updated last week
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆79Updated 11 months ago
• ryanlayer / stix
  Structural Variant Index
  ☆71Updated last month
• refgenie / refgenie
  Reference genome resource manager
  ☆73Updated last year
• gatk-workflows / broad-prod-wgs-germline-snps-indels
  Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…
  ☆56Updated 4 years ago
• biowdl / tasks
  A collection of reusable WDL tasks. Category:Other
  ☆85Updated this week
• imgag / ClinCNV
  Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
  ☆80Updated last week
• RCollins13 / CNView
  Visualization and annotation of CNVs from population-scale whole-genome sequencing data
  ☆69Updated 7 years ago
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• Clinical-Genomics / MIP
  Mutation Identification Pipeline. Read the latest documentation:
  ☆44Updated 10 months ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆137Updated 8 months ago
• ewels / AWS-iGenomes
  Documentation and description of AWS iGenomes S3 resource.
  ☆109Updated last month
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 2 years ago
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆101Updated 4 years ago
• naumanjaved / fingerprint_maps
  Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of func…
  ☆26Updated last year
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆103Updated 4 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆55Updated last year
• Clinical-Genomics / stranger
  Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat
  ☆31Updated 2 months ago
• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆48Updated 5 years ago
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆74Updated last year
• genome-in-a-bottle / giab_latest_release
  This repository contains information about latest release from Genome in a Bottle project
  ☆73Updated 5 years ago
• deaconjs / ThousandVariantCallersRepo
  Thousand Variant Callers Project Repository
  ☆71Updated 5 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆41Updated 9 years ago