All Published Workflows

76 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
nbis-meta
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A snakemake workflow for metagenomic projects
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public

A workflow for metagenomic projects A snakemake workflow for paired- and/or single-end whole-genome shotgun metagenomic d...
Barrnap prodigal MEGAHIT Biopython BLAST Bowtie 2 Centrifuge CheckM contigtax Cutadapt edgeR eggNOG-mapper v2 FastANI FastQC FeatureCounts Infernal cmscan (EBI) kraken2 Krona MaxBin MetaBAT 2 metagenomeSeq MetaPhlAn metaspades MultiQC Pandas Picard SAMtools seqtk Snakemake SortMeRNA SqueezeMeta Trimmomatic Trnascan-SE CONCOCT common gtdbtk networkx numpy RGI
Free
137
evidence_datasource_parsers
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script to convert phewascatalog database to JSONs, with ENSGIDs and EFO ids.
public

public

This repository contains a collection of modules which generate evidence for several internal data sources (“internal” meanin...
JSON Pandas Snakemake common requests scipy
Free
43
bioconda-paper
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Data analysis related to the bioconda paper
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public

This Snakemake workflow automatically generates all results and figures from the Bioconda paper. Any 64-bit Linux installatio...
JSON Pandas Snakemake common matplotlib networkx numpy seaborn svgutils
Free
41
dna-seq-benchmark
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A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets
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public

A Snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB) data (and other custom benchm...
JSON Gene ID Variant calling genetic variants snakemake-wrapper-utils BCFtools BEDTools BWA mosdepth Pandas Picard RTG Core SAMtools Snakemake common numpy pysam scipy sklearn statsmodels Genomics
Free
48
varlociraptor-evaluation
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Snakemake workflow for evaluating varlociraptor
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public

This Snakemake workflow automatically generates all results and figures from the initial Varlociraptor paper focusing on so...
delly rust-bio-tools BamTools BCFtools BWA cyvcf2 Pandas Picard SAMtools Snakemake UpSetR ggplot2 plyr rlist common matplotlib networkx numpy pysam seaborn Varlociraptor
Free
90
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
qcsd-experiments
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QCSD: A QUIC Client-Side Website-Fingerprinting Defence Framework
public

public

This repository contains the experiment and evaluation code for the paper "QCSD: A QUIC Client-Side Website-Fingerprinting De...
JSON BiocSklearn Pandas Snakemake TensorFlow aiohttp common h5py lab matplotlib networkx numpy publicsuffixlist PyYAML scipy seaborn sklearn tslearn
Free
48
stratomod
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StratoMod: Quantifying the Difficulty of Variant Calling in Genomic Context
public

public

A model-based tool to quantify the difficulty of calling a variant given genomic context. Intuitively we understand that accu...
JSON Quantification Variant calling tabix BEDTools Biopython CAT Pandas Pybedtools RTG Core SAMtools Snakemake ggplot2 ggpubr infotheo tidyverse common more-itertools numpy PyYAML sklearn typing-extensions Genomics
Free
83
nanopore-qc
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A quality control pipeline for Oxford Nanopore sequencing
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public

Johannes Köster (@johanneskoester) If you simply want to use this workflow, download and extract the latest release ...
JSON porechop CRIMSON FastQC Kraken Pandas Snakemake common h5py matplotlib networkx numpy seaborn
Free
21
active-strs-analysis
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Short Tandem Repeat (STR) Catalog Analysis Workflow
public

public

Active STRs Analysis This repository contains a Snakemake workflow for analyzing the regulatory and functional role of short ...
JSON BEDTools Pandas Snakemake TRF common pyliftover pysam utils Sequence analysis
Free
26
fastdrep
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Snakemake workflow to cluster genomes (e.g. Metagenome assembled genomes) into species and Strains
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public

Silas Kieser (@silask) Webpage If you simply want to use this workflow, download and extract the latest release ...
Mash Minimap2 Pandas Snakemake common networkx numpy scipy sklearn
Free
19