All Published Workflows

3 workflows that have been reviewed and published

mtoolbox_snakemake
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MToolBox pipeline written in snakemake to allow a better scalability
public

public

This is an work-in-progress update of MToolBox ( PMID:25028726 ). Please find more at the official documentation .
VCF raw sequence reads Genetic mapping Alignment gatk BCFtools FastQC Picard SAMtools Snakemake Trimmomatic Genomics
Free
22
mtb-call
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M. tuberculosis variant identification (deprecated 2023). Use: https://github.com/ksw9/mtb-vars
public

public

Snakemake pipeline for M. tuberculosis variant identification from short-read data, mapping with bwa, variant identificat...
TSV Sample annotation Genetic mapping Report tabix BCFtools mosdepth Sambamba Snakemake snpEff Trim_Galore Genetic variation
Free
13
sqtlseeker2-nf
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The Nextflow pipeline for Splicing Quantitative Trait Loci (sQTL) mapping
public

public

A pipeline for splicing quantitative trait loci (sQTL) mapping. Splicing quantitative trait loci mapping is a technique used ...
CSV Gene expression matrix Genetic mapping genetic variants sqtlseeker2-nf sQTLseekeR2 splicing quantitative trait loci mapping
Free
8