MONSDA: Modular Organizer of Nextflow and Snakemake driven HTS Data Analysis

Abstract

MONSDA runs HTS data analysis from pre- to postprocessing based on a single configuration file. It wraps Snakemake or Nextflow to run workflow steps involving QC, trimming, mapping, deduplication and differential analysis as well as a set of specific workflows for the generation of genome browser tracks and more. Users profit from many of the advantages of two of the most popular workflow management systems without having to learn all the specifics of Snakemake or Nextflow and can interchange and configure tools according to their specific needs. MONSDA is available via Bioconda, pip and https://github.com/jfallmann/MONSDA

Toward a Systematic Assessment of Sex Differences in Cystic Fibrosis

“…The downloading, processing, and analysis of the data used in this study were conducted using MONSDA [ 20 ] release v1.1.0 . The corresponding configuration file is available at , accessed on 26 May 2023.…”

“…The downloading, processing, and analysis of the data used in this study were conducted using MONSDA [20] release v1.1.0. The corresponding configuration file is available at https://raw.githubusercontent.com/jfallmann/MONSDA_companion/main/ CysticFibrosisGenderBias/config_cystic_fibrosis_monsda.json, accessed on 26 May 2023.…”