Open JensUweUlrich opened 1 year ago
Thanks for your interest.
KMCP is only suitable for short-read metagenomic profiling, with much lower sensitivity on long-read datasets. My initial plan was to support both short and long reads. But the read matching strategy, i.e., keeping reads with enough (>= 50% ) k-mers contained in a genome chunk, is of low sensitivity for long reads, even for HIFI reads.
Some strategies were tried, but the results were out of expectation.
The answer is added to FAQs page: https://bioinf.shenwei.me/kmcp/faq/#does-kmcp-support-long-read-metagenomic-profiling
Dear Wei Shen, I really like your tool and your tutorials. I just have a question regarding long read metagenomic profiling. Is there a specific parameter combination you would recommend to use to taxonomic profiling? It seems like I'm missing some organisms from the Zymo Mock Community even when using profiling mode m=0. Thanks Jens