lncRNApipe is a reference annotation based automated pipeline to identify non-coding RNAs, both known and novel from RNA-Seq reads. It takes FASTQ / FASTA reads as input, trims reads, assembles transcripts, and identifies any possible known and novel ncRNAs, categorizes them into 5 catgories: Long intergenic lncRNAs (LincRNAs), Intronic contained lncRNAs (Incs), Partially overlapping lncRNAs (Poncs), Completely overlapping lncRNAs (Concs) and Exonic overlaps (LncRNAs with sense or antisense overlap with reference exon) and annotates the novel ncRNAs, where possible.
The source code is freely available at github.com
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