All Published Workflows

50 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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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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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
sv-callers
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Snakemake-based workflow for detecting structural variants in genomic data
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Structural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases. sv-ca...
raw sequence reads Variant calling genetic variants delly BCFtools GRIDSS Snakemake Viola SURVIVOR Genomics
Free
13
svdss
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Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)
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public

Note: for SVDSS (v1), please refer to v1.0.5-fix and 6fa89f0 . SVDSS is a novel method for discovery of structural...
Sample annotation Variant calling genetic variants BCFtools SAMtools Snakemake Structural variation
Free
4
varca
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Use an ensemble of variant callers to call variants from ATAC-seq data
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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
uncovar
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Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
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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
rna-seq-pop
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Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
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Documentation : https://sanjaynagi.github.io/rna-seq-pop/ Walkthrough : https://www.youtube.com/watch?v=5QQe7DLHO4...
FASTQ-illumina JSON Sample annotation Variant calling genetic variants snakemake-wrapper-utils EnhancedVolcano BCFtools DESeq2 fastp FreeBayes GLUE HISAT2 kallisto mosdepth MultiQC Pandas pheatmap Quant SAMBLASTER SAMtools sleuth Snakemake snpEff Vcflib data.table dplyr ggplot2 ggrepel jsonlite openxlsx RColorBrewer tidyverse ipykernel matplotlib matplotlib-venn numpy papermill pop-tools scipy zarr Population genomics
Free
63
dna-seq-neoantigen-prediction
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Neoantigen Prediction Snakemake Workflow: Genomic Variant Detection and Peptidome Incorporation
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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
hifitargetenrichment
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A repo for the Twist HiFi capture/snakemake workflow
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This is a snakemake workflow for analyzing targeted HiFi sequence datasets. The workflow was designed for Twist gene pane...
FASTQ VCF raw sequence reads Variant calling genetic variants snakemake-wrapper-utils tabix BEDTools MLM Pandas Picard SAMtools Snakemake GLnexus matplotlib numpy seaborn Gene regulation
Free
66
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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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
rnaseq_variant_calling_workflow
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This is an human RNAseq variant calling workflow, following the GATK pipeline. Also includes ADAR-site elimination.
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Clone the git repository with the command: git clone https://github.com/durrantmm/rnaseq_variant_calling_workflow.git This wo...
raw sequence reads Variant calling genetic variants tabix BEDTools SAMtools Snakemake STAR VCFtools RNA-Seq
Free
18
samosa
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(S)train (A)ssignment from (M)etagen(O)me (S)NP (A)nalysis.
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SAMOSA is a Snakemake computational workflow for performing strain level detection from Metagenomic samples. The pipeline is ...
FASTQ Sample annotation Variant calling genetic variants gatk Bowtie 2 FreeBayes Picard SAMtools Snakemake Trimmomatic Metagenomic sequencing
Free
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