ncRNA Discovery

The novel ncRNA branch uses non-host reads together with the optional assembly FASTA and GFF.

Main stages: - build Bowtie index on the assembly - map reads to contigs - extract strand-aware BED intervals - cluster supported loci - remove overlaps with existing annotations - retain intergenic and antisense-to-CDS candidates - optionally filter candidates against Rfam and fold them with RNAfold

Key summary output: - <sample>.novel.summary.tsv