nf-rnaSeqMetagen

Metagenomics focuses on identifying microbial genomes in environmental samples, particularly non-host sequences within a host genome. This study developed the nf-rnaSeqMetagen pipeline to efficiently identify and characterize microbial reads from RNA-seq data. Using Nextflow for workflow management and Singularity for containerization, the pipeline filters out host reads and analyzes exogenous reads with the kraken2 database. Tested on RNA-seq data from systemic sclerosis (SSc) patients, it identified clinically relevant bacteria such as Arthrobacter and Bacillus. The pipeline is adaptable for various platforms and available on GitHub.
Mpangase et al. 2020 Med Microecol 4: 1…