Intuitions regarding possible output and previous steps about plass

[martin-steinegger]

@adriaaula thank you for trying out Plass and your comments. :)

I agree at 20X increase seems to be too high. We used --cov-mode 1 to cluster the proteins in the Plass paper and we only consider assembled proteins(fragments) with length > 100. This mode should merge small fragments. The mode you picked --cov-mode 2 clusters only sequences that can cover the center sequence by 90%. Therefor you end up with many protein fragments. See https://github.com/soedinglab/MMseqs2/wiki#how-to-set-the-right-alignment-coverage-to-cluster

We did not perform quality trimming for the publication but we downloaded quality filtered data from the JGI site. The filtering was preformed by RQCFilter https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/data-preprocessing/

In general quality filtering of metagenomic data is tricky. I have tested Plass in combination with bloocoo (https://github.com/GATB/bloocoo) to correct errors and I could see an slight increase in precision and sensitivity of the assembly. So I can recommend using it. Trimming could improve the recovery of some low abundant proteins if the error affect the most left or right amino acid. For highly abundant species (o proteins) trimming will not have too much of an effect, since Plass will pick the best extension by considering sequence identity and thus bogus fragments will be discarded by the lack of homology.