Alternatives and similar repositories for workflows:

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

• dputhier / pygtftk
  A python package and a set of shell commands to handle GTF files
  ☆48Updated 10 months ago
• TrinityCTAT / ctat-mutations
  Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
  ☆74Updated 9 months ago
• SciLifeLab / NGI-RNAseq
  Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
  ☆51Updated 6 years ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆47Updated this week
• chanzuckerberg / idseq-workflows
  Portable WDL workflows for IDseq production pipelines
  ☆31Updated 3 years ago
• 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 PairedEndSingleSampleWf has been superseded in Broad production by https://gi…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 5 years ago
• YeoLab / outrigger
  Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
  ☆65Updated 5 years ago
• Oshlack / Clinker
  Gene Fusion Visualiser
  ☆51Updated 2 years ago
• pinellolab / AmpUMI
  Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)
  ☆41Updated last year
• CGGOxford / Opossum
  Opossum is a tool to pre-process RNA-seq reads prior to variant calling.
  ☆28Updated 6 years ago
• stjude / CICERO
  CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
  ☆38Updated 2 weeks ago
• s-andrews / BamQC
  Mapped QC analysis program
  ☆44Updated 6 years ago
• grst / snakemake_nextflow_wdl
  simple comparison of snakemake, nextflow and cromwell/wdl
  ☆49Updated 4 years ago
• smithlabcode / preseq
  Software for predicting library complexity and genome coverage in high-throughput sequencing.
  ☆82Updated 6 months ago
• deaconjs / ThousandVariantCallersRepo
  Thousand Variant Callers Project Repository
  ☆72Updated 5 years ago
• nf-core / oncoanalyser
  A comprehensive cancer DNA/RNA analysis and reporting pipeline
  ☆67Updated last week
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆50Updated 4 years ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 2 months ago
• tk2 / RetroSeq
  RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…
  ☆66Updated 2 years ago
• genepi / nf-gwas
  A nextflow pipeline to perform state-of-the-art genome-wide association studies.
  ☆67Updated last month
• stjudecloud / wdldoc
  Create WDL documentation using Markdown.
  ☆27Updated last month
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆41Updated 9 years ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆140Updated 3 weeks ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆96Updated last year
• seppinho / mutserve
  mtDNA Variant Caller
  ☆34Updated 4 months ago
• SciLifeLab / TIDDIT
  TIDDIT - structural variant calling
  ☆73Updated 3 weeks ago
• PapenfussLab / sv_benchmark
  Comprehensive benchmark of structural variant callers
  ☆46Updated 4 years ago
• sigven / cpsr
  Cancer Predisposition Sequencing Reporter (CPSR)
  ☆58Updated last month
• 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…
  ☆44Updated 2 years ago
• grocsvs / grocsvs
  Genome-wide reconstruction of complex structural variants
  ☆39Updated 2 years ago