All Published Workflows

3 workflows that have been reviewed and published

dna-seq-neoantigen-prediction
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Neoantigen Prediction Snakemake Workflow: Genomic Variant Detection and Peptidome Incorporation
public

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
eager
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A fully reproducible and state-of-the-art ancient DNA analysis pipeline
public

public

A fully reproducible and state-of-the-art ancient DNA analysis pipeline . nf-core/eager is a scalable and reproducible...
JSON Sequence trace Genetic variation analysis Data angsd gatk mtnucratio pmdtools preseq vcf2genome AdapterRemoval AMPS BBMap BCFtools BEDTools Bowtie 2 BWA fastp FastQC FreeBayes gatk_realigner_target_creator kraken2 MapDamage MultiQC Picard QualiMap SAMtools Malt DNA Sequence analysis
Free
101
sars-cov-2-pe-illumina-artic-variant-calling-covid
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COVID-19: variation analysis on ARTIC PE data
public

public

The workflow for Illumina-sequenced ampliconic data builds on the RNASeq workflow for paired-end data using the same steps fo...
Gene ID Genetic variation analysis genetic variants BCFtools BWA fastp Galaxy iVar lofreq MultiQC QualiMap SAMtools snpEff Vcflib WorkflowHub COVID19 Risk Mitigation
Free