Alternatives and similar repositories for workflows:

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

• chanzuckerberg / idseq-workflows
  Portable WDL workflows for IDseq production pipelines
  ☆31Updated 3 years ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆45Updated this week
• stjudecloud / wdldoc
  Create WDL documentation using Markdown.
  ☆27Updated this week
• 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 PairedEndSingleSampleWf has been superseded in Broad production by https://gi…
  ☆55Updated 4 years ago
• Clinical-Genomics / MIP
  Mutation Identification Pipeline. Read the latest documentation:
  ☆44Updated 11 months ago
• grst / snakemake_nextflow_wdl
  simple comparison of snakemake, nextflow and cromwell/wdl
  ☆50Updated 4 years ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated last week
• nf-core / oncoanalyser
  A comprehensive cancer DNA/RNA analysis and reporting pipeline
  ☆59Updated this week
• Oshlack / Clinker
  Gene Fusion Visualiser
  ☆51Updated 2 years ago
• stjude / CICERO
  CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
  ☆36Updated last month
• SciLifeLab / TIDDIT
  TIDDIT - structural variant calling
  ☆74Updated last month
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆75Updated last year
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆137Updated 8 months ago
• wdecoster / nano-snakemake
  A snakemake pipeline for SV analysis from nanopore genome sequencing
  ☆51Updated 4 years ago
• genepi / nf-gwas
  A nextflow pipeline to perform state-of-the-art genome-wide association studies.
  ☆64Updated 2 months ago
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated last year
• cancerit / alleleCount
  Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…
  ☆43Updated 2 years ago
• xuchang116 / smCounter
  smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very…
  ☆20Updated 5 years ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆84Updated 6 years ago
• pwwang / vcfstats
  Powerful statistics for VCF files
  ☆68Updated last year
• PacificBiosciences / HiFi-human-WGS-WDL
  ☆55Updated this week
• sigven / gvanno
  Generic human DNA variant annotation pipeline
  ☆57Updated last year
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆38Updated 3 years ago
• Clinical-Genomics / stranger
  Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat
  ☆32Updated 2 months ago
• brentp / jigv
  igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
  ☆126Updated last year
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆96Updated 2 years ago
• TrinityCTAT / ctat-mutations
  Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
  ☆74Updated 7 months ago
• Oshlack / STRetch
  Method for detecting STR expansions from short-read sequencing data
  ☆62Updated 3 years ago
• CGGOxford / Opossum
  Opossum is a tool to pre-process RNA-seq reads prior to variant calling.
  ☆28Updated 6 years ago
• tommyau / bamclipper
  Remove primer sequence from BAM alignments by soft-clipping
  ☆31Updated 5 years ago