As noted in the docstrings for the rules, there are some applications (like peptide discovery) that require short contigs. While most of these contigs will be fragments (aberrant transcription, degraded RNA, broken assembly), some will represent true peptides. There are specific methods for identifying when this is the case which are probably outside of the scope of this repo & of reads2transcriptome, but outputting these short contigs will allow people to explore them for real biological signal.
As noted in the docstrings for the rules, there are some applications (like peptide discovery) that require short contigs. While most of these contigs will be fragments (aberrant transcription, degraded RNA, broken assembly), some will represent true peptides. There are specific methods for identifying when this is the case which are probably outside of the scope of this repo & of
reads2transcriptome, but outputting these short contigs will allow people to explore them for real biological signal.