snakemake-workflows/dna-seq-gatk-variant-calling

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snakemake-workflows/dna-seq-gatk-variant-calling

snakemake-workflows

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This Snakemake pipeline implements the GATK best-practices workflow

Snakemake workflow: dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants.

Usage

The usage of this workflow is described in the Snakemake Workflow Catalog.

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and its DOI (see above).

rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

docs

Documentation of the Snakemake-Workflows project

single-cell-rna-seq

A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.

snakemake-workflow-template

A template for standard compliant snakemake-workflows

dna-seq-varlociraptor

A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.

rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

cookiecutter-snakemake-workflow

A cookiecutter template for Snakemake workflows

chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).

ngs-test-data

A workflow for creating small NGS test data sets, useful for continuous integration.

dna-seq-neoantigen-prediction

Snakemake workflow for neoantigen prediction

dna-seq-benchmark

A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets

dna-seq-mtb

A flavor of https://github.com/snakemake-workflows/dna-seq-varlociraptor preconfigured for molecular tumor boards

cyrcular-calling

A Snakemake workflow for ecDNA detection in Nanopore or Illumina sequencing reads derived from DNA samples enriched for circular DNA.

species-quantification

cite-seq-alevin-fry-seurat

Snakemake workflow for CITE-seq analaysis with alevin-fry and seurat

transcriptome-differential-expression

long read differential expression analysis

rad-seq-stacks

structure-based-screening

Workflow for screening massive amounts of small molecules (ligands) against a target (PDB-File)