All Published Workflows

25 workflows that have been reviewed and published

dna-seq-gatk-variant-calling
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This Snakemake pipeline implements the GATK best-practices workflow
public

public

This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
VCF raw sequence reads Variant calling genetic variants gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BWA FastQC MultiQC Pandas Picard SAMtools Snakemake Trimmomatic Variant Effect Predictor (VEP) common matplotlib numpy seaborn DNA
Free
57
dna-seq-varlociraptor
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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.
public

public

A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse...
JSON raw sequence reads Variant calling genetic variants delly gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BEDTools Bowtie 2 BWA Cutadapt FastQC fgbio FreeBayes mosdepth MultiQC Pandas Picard SAMtools Snakemake Variant Effect Predictor (VEP) vembrane numpy oschmod sklearn statsmodels Varlociraptor DNA
Free
127
iguide
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Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.
public

public

Bioinformatic pipeline for processing iGUIDE and GUIDE-seq samples. iGUIDE is a pipeline written in snakemake for proc...
Data Read pre-processing Report Biostrings BSgenome BWA Quant SAMtools Snakemake magrittr DNA
Free
65
benchmark-giab
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A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets
public

public

A Snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB) data (and other custom benchm...
JSON File name Variant calling genetic variants snakemake-wrapper-utils BCFtools BEDTools BWA mosdepth Pandas Picard RTG Core SAMtools Snakemake common numpy pysam scipy sklearn statsmodels DNA
Free
48
gatk-snakemake-pipeline
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DNA-seq and Neoantigens prediction
public

public

Snakemake workflow for neoantigen prediction. This workflow is still in development This snakemake pipeline implement...
JSON Sample annotation Genome annotation Genome report gatk BWA fastp Picard razers3 SAMtools Snakemake DNA Genomics
Free
28
ancient-microbiome-smk
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aMeta: Ancient DNA Shotgun Metagenomics Analysis Workflow
public

public

aMeta is a Snakemake workflow for identifying microbial sequences in ancient DNA shotgun metagenomics samples. The workflow p...
pmdtools AMPS Bowtie 2 Cutadapt FastQC KrakenUniq Krona MapDamage MultiQC SAMtools seqtk Snakemake subSeq Malt DNA metagenomics
Free
31
qdnaseq-snakemake
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Installation and Execution Guide for QDNAseq.snakemake Pipeline
public

public

For the installation of this pipeline any Python install compatable Conda is required. The pipeline itself will run on Python...
Biobase BWA CGHcall CGHregions FastQC GTools impute limma Picard QDNAseq SAMtools Snakemake denstrip MASS R.cache readxl stringr DNA
Free
34
orochi
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Orochi: Metagenomic Analysis Pipeline for DNA Samples
public

public

Orochi is a Snakemake-based metagenomic analysis pipeline designed to perform a full-featured analysis of metagenomic DNA sam...
JSON bigslice prodigal antiSMASH BBMap Biopython BWA CAT cd-hit CoverM DAS Diamond eggNOG-mapper v2 hmmsearch (genouest) MetaBAT 2 Minimap2 SAMtools seqtk Snakemake Trimmomatic VAMB CONCOCT DNA metagenomics
Free
64
workflow_obitools
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DNA Metabarcoding Data Analysis Workflow with Obitools Suite
public

public

This is a snakemake workflow based on the obitools suite of programs, that analyzes DNA metabarcoding data. Sequence analysis...
sumaclust Cutadapt OBITools Snakemake DNA
Free
15
workflow_obitools_ecofeed
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DNA Metabarcoding Data Analysis Using Obitools and Snakemake on a Cluster
public

public

This is a snakemake workflow based on the obitools suite of programs, that analyzes DNA metabarcoding data. Sequence analysis...
sumaclust Cutadapt OBITools Snakemake DNA
Free
15
fusarium_workflow
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Fusarium Genome DNA-seq QC, Alignment, and Variant Calling Workflow Using Snakemake
public

public

Fusarium_workflow A basic snakemake file for QC, Alingment and Variant calling on DNAseq data of F.oxy.genome needs conda and...
Sequence alignment Variant calling gatk Bowtie 2 fastp FastQC Picard SAMtools Snakemake DNA
Free
12
variantcallingwithsnakemake
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Genome Re-sequencing Analysis Snakemake Workflow: De-novo and Variant Calling Modes
public

public

This Snakemake workflow is for analysing genome re-sequencing experiments. It features 2 modes. The **de-novo** mode is used ...
JSON Sequence analysis Variant calling seqhax AdapterRemoval BCFtools BWA FreeBayes kWIP Mash QualiMap SAMtools Snakemake snpEff rgl matplotlib numpy pysam tqdm DNA Sequence analysis
Free
41