All Published Workflows

228 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.
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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
mapache
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mapping pipeline for ancient DNA
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public

Mapache ([maˈpa.t͡ʃe]) is a lightweight mapping pipeline for ancient DNA using the workflow manager Snakemake . Visit ...
BAM Sample ID Mapping Report gatk tabix AdapterRemoval BCFtools BEDTools Bowtie 2 BWA fastp FastQC gatk_realigner_target_creator MapDamage MultiQC Pandas Picard QualiMap SAMtools seqtk Snakemake GLIMPSE numpy Comparative genomics
Free
95
snparcher
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Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
public

public

snpArcher is a reproducible workflow optimized for nonmodel organisms and comparisons across datasets, built on the Snakema...
CleanEx dataset code Variant calling Quality control report gatk genmap tabix BCFtools BEDTools BWA fastp mosdepth Picard Sambamba SAMtools Sentieon DNASeq Snakemake Data quality management
Free
40
human_genomics_pipeline
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A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
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A Snakemake workflow to process single samples (unrelated individuals) or cohort samples (related individuals) of paired-end ...
FASTQ raw sequence reads Sequencing quality control Haplotype map gatk BWA FastQC MultiQC Snakemake Trim_Galore Genomics
Free
14
ngs-pipeline
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Pipeline for Somatic Variant Calling with WES and WGS data
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public

Somatic variant calling pipeline for whole exome and whole genome sequencing (WES & WGS). The pipeline uses Mutect2 to identi...
gatk BWA FastQC mosdepth MultiQC Pandas SAMtools Snakemake dplyr ggplot2 readr
Free
32
dna-seq-neoantigen-prediction
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Neoantigen Prediction Snakemake Workflow: Genomic Variant Detection and Peptidome Incorporation
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public

This workflow detects genomic variants with Strelka and and tries to incorporate germline and somatic variants into a sam...
Sequence Genetic variation analysis genetic variants gatk hla-la rust-bio-tools tabix Arriba BCFtools BWA Cutadapt FreeBayes kallisto Microphaser NetMHCIIpan NetMHCpan Pandas Picard Quant razers3 SAMtools Snakemake STAR Strelka Variant Effect Predictor (VEP) vembrane Jinja2 numpy Varlociraptor Genomics
Free
122
bo-demography
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Demographic analysis of Brassica oleracea
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public

Demographic analysis of Brassica oleracea Follows GATK4 best practices (https://software.broadinstitute.org/gatk/best-practic...
gatk tabix BCFtools BEDTools BWA CLICK FastQC MultiQC Pandas QualiMap SAMtools Snakemake VCFtools cowplot ggplot2 tidyverse
Free
49
genome-seek
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Clinical Whole Genome Sequencing Pipeline
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public

Whole Genome Clinical Sequencing Pipeline. This is the home of the pipeline, genome-seek. Its long-term goals: to ac...
gatk hla-la peddy tabix AnnotSV BCFtools Bowtie 2 Bwa-mem2 fastp FastQC gatk_realigner_target_creator MultiQC NG-Circos octopus Pandas Picard QualiMap SAMBLASTER SAMtools Singularity Hub Snakemake VCFtools GLnexus
Free
57
hribo
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HRIBO: High-throughput annotation by Ribo-seq workflow for analyzing bacterial Ribo-seq data
public

public

We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of ...
Sequence Sequence annotation ORF ID gatk ucsc-bigwigtowig BEDTools Cutadapt FastQC FeatureCounts GFFutils MultiQC Picard SAMtools Snakemake wigToBigWig bacterial assembly and annotation
Free
154
germlinemutationcalling
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An adaptable Snakemake workflow which uses GATKs best practice recommendations to perform germline mutation calling starting with BAM files
public

public

This Snakemake workflow follows the GATK best-practice recommandations to call small germline variants. The pipeline requ...
gatk Snakemake
Free
16
hemomips
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Automated analysis and result reporting for targeted sequencing data
public

public

The hemoMIPs pipeline is a fast and efficient analysis pipeline for the analysis of multiplexed and targeted NGS datasets cre...
gatk tabix BEDTools BWA SAMtools Snakemake Variant Effect Predictor (VEP) pysam
Free
33