kmcp
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shenwei356
Accurate metagenomic profiling && Fast large-scale sequence/genome searching
Automatically disable ambiguous-matches correction for complex communities with thousands of species
It's optional for now, but it would be better to be switched on automatically to reduce profiling time. ``` $ kmcp profile -h Generate taxonomic profile from search results Methods:...
Dear Shenwei, Thank you very much for providing a good tool, I am trying to adjust the output table as desired according to KMCP format. - Currently I use search...
Test kmcp with mock community datasets. The result is like this. 
The current tab-delimited search result format is redundant and [inefficient](https://github.com/shenwei356/kmcp/issues/38#issuecomment-1704007482) for parsing in `kmcp profile`. So we can use a compact binary format to save the temporary result. 1. `kmcp...
Hello Shenwei, Thank you for making this new metagenomic tool! I'm interested in benchmarking its performance, and for that I want to perform classification on a large (10,000+) number of...
Just a suggestion for the [database build step](https://bioinf.shenwei.me/kmcp/database/#gtdb). Since the sample size is pretty big, it's worth using the [`--enable-score-calibration` in geNomad](https://portal.nersc.gov/genomad/score_calibration.html). This parameter substantially improves the classification accuracy and...
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...
Hey there, @shenwei356 :) Thanks again for not only additional wonderful software, but excellent documentation as usual! I'm looking for a better way to taxonomically classify predicted coding sequences and...
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Accurate metagenomic profiling && Fast large-scale sequence/genome searching