Sylph unable to profile low coverage SAGs

[lingrongjin]

I'm trying to use sylph to profile single cell amplified genomes (SAGs); however, I found that many of my SAG sample files do not pass the profiling threshold. I tried profiling over pre-built gtdb database and sylsp database built from MAGs and SAGs assembled from the same samples, but only 2700 out of ~17000 SAGs with >10000 clean reads can be profiled by sylph. I'm wondering what can be the causes of the low classification rate - from my understanding, most SAGs represent single-species bacterial genomes, and with around ~10000 reads, sylph should be able to classify them if they are represented in the database?

[bluenote-1577]

@lingrongjin there are a few things that come to mind

• I've never profiled with single cell sequencing, but the coverage distribution is -- from my understanding -- very skewed compared to metagenomics. sylph assumes a metagenomics-like read coverage distribution across the genome
• are you sure the SAGs have a species-level representative in GTDB? sylph can only do species-level profiling well, so if your SAG is a new species, sylph won't work.
• you can try doing -m 85; this will check if there are genomes in the database present with > 85% ANI to your SAG (very approximate/rough)