Software pipelines for RNA-Seq, ChIP-Seq and germline variant calling analyses in common workflow language (CWL).

ABSTRACT: Background: Automating data analysis pipelines is a key requirement to ensure reproducibility of results, especially when dealing with large volumes of data. Here we assembled automated pipelines for the analysis of High-throughput Sequencing (HTS) data originating from RNA-Seq, ChIP-Seq and Germline variant calling experiments. We implemented these workflows in Common workflow language (CWL) and evaluated their performance by: i) reproducing the results of two previously published studies on Chronic Lymphocytic Leukemia (CLL), and ii) analyzing whole genome sequencing data from four Genome in a Bottle Consortium (GIAB) samples, comparing the detected variants against their respective golden standard truth sets. Findings: We demonstrated that CWL-implemented workflows clearly

SUBMITTER: Kyritsis KA 

PROVIDER: S-EPMC10662043 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature