nf-rnaSeqMetagen

nf-rnaSeqMetagen performs taxonomic identification and classification of microbial (non-host) reads from high-throughput RNA sequencing (RNA-seq) data to detect exogenous microorganisms within host-derived samples.

Key Features:

• Nextflow Integration: Uses Nextflow for workflow management and process orchestration, handling dataflow between processes.
• Singularity Containerization: Packages all applications in Singularity containers to enable parallel execution, portability, and reproducibility.
• Host Read Filtering: Filters out reads belonging to the host organism to retain exogenous microbial sequences.
• Taxonomic Classification: Classifies non-host reads using kraken2 with a database constructed from bacterial, archaeal, and viral genomes.

Scientific Applications:

• Systemic sclerosis (SSc) skin microbiome analysis: Applied to RNA-seq from SSc patient skin samples to identify potential pathogens, detecting bacterial genera including Arthrobacter, Bacillus, Brachybacterium, Dietzia, and Pseudarthrobacter.
• General RNA-seq metagenomics: Adapted for broader metagenomics studies to detect microbial associations in host-derived RNA-seq datasets.

Methodology:

Implemented in Nextflow with Singularity containers, the pipeline performs host read filtering on RNA-seq data and applies kraken2 taxonomic classification using a database of bacterial, archaeal, and viral genomes.