All Published Workflows

231 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
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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
lathe
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A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
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public

A tool for generating bacterial genomes from metagenomes with Nanopore long read sequencing First, install miniconda3 The...
bacterial Base-calling Sample annotation mummer2circos tabix BCFtools BEDTools BWA CANU Consensus Flye GUPPY Medaka Minimap2 NanoPlot pilon Racon SAMtools Snakemake pysam metagenomics
Free
39
covid-19-signal
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Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
public

public

This is a complete standardized workflow the assembly and subsequent analysis for short-read viral sequencing. This core work...
FASTQ-illumina Query script Genome assembly Taxonomic classification tabix BCFtools BEDTools breseq BWA Consensus FastQC FreeBayes iVar kraken2 Pangolin QUAST SAMtools Snakemake vt Trim_Galore COVID19 Risk Mitigation
Free
31
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
varca
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Use an ensemble of variant callers to call variants from ATAC-seq data
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public

A pipeline for running an ensemble of variant callers to predict variants from ATAC-seq reads. The entire pipeline is made up...
VCF Data Variant calling genetic variants delly macs2 tabix BCFtools BEDTools BWA Pandas SAMtools Snakemake BBmisc data.table dplyr ggplot2 parallelMap plyr R.devices matplotlib numpy pysam sklearn ATAC-seq deep learning
Free
39
snparcher
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Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
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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
uncovar
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Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
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public

A reproducible and scalable workflow for transparent and robust SARS-CoV-2 variant calling and lineage assignment with com...
JSON raw sequence reads Variant calling genetic variants delly nanofilt rust-bio-tools snakemake-wrapper-utils tabix BCFtools Biopython BWA CANU Consensus fastp FastQC fgbio FreeBayes GFFutils kallisto Kraken Krona Medaka metaspades Minimap2 MultiQC Pandas Pangolin Picard Quant QUAST SAMtools Snakemake Variant Effect Predictor (VEP) vembrane altair intervaltree numpy pysam requests Varlociraptor COVID19 Risk Mitigation
Free
204
mosaicatcher-pipeline
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Integrated workflow for SV calling from single-cell Strand-seq data
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public

Structural variant calling from single-cell Strand-seq data Snakemake pipeline. This workflow uses Snakemake to execu...
mosaicatcher tabix BCFtools BEDTools ComplexHeatmap Pandas pheatmap SAMtools Snakemake TensorFlow WhatsHap assertthat BiocManager cowplot data.table devtools dplyr ggnewscale ggplot2 ggpubr matrixStats optparse RColorBrewer reshape reshape2 scales stringr tibble tidyr intervaltree matplotlib numpy parmap plotly pysam PyYAML scipy seaborn tqdm xopen
Free
202
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