Inputs and Outputs

Required Inputs

Required per sample: - one raw, non-filtered single-end smallRNA FASTQ file - host reference FASTA files or prebuilt host Bowtie indexes

Optional Inputs

Optional per sample: - assembly FASTA - assembly GFF

Main Output Groups

For each sample, the pipeline writes: - preprocessing FASTQs and QC files - host analysis outputs - non-host analysis outputs - assembly-based outputs - novel ncRNA outputs - summary TSVs - MultiQC report