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Wei Shen 沈 伟 Profile picture
Wei Shen 沈 伟
@shenwei356
Associate professor of Bioinformatics at Chongqing Medical University, China. Developing tools for microbial (meta)genomics. https://t.co/InKboveXni
Dec 30, 2022 • 11 tweets • 3 min read
🎉KMCP is out in Bioinformatics. In the paper we present a novel k-mer-based metagenomic profiling tool that combines k-mer similarity and genome coverage information to increase the profiling accruacy.
academic.oup.com/bioinformatics… KMCP splits the ref genomes into chunks and stores k-mers in a optimized COBS index for fast alignment-free sequence searching. Like quasi-mapping in RapMap, we tracks the target and position for each query. However, the read position is approximate and in a predefined resolution
Mar 9, 2022 • 13 tweets • 5 min read
Can't wait to share the KMCP preprint with you, hope it's not too late. Thanks for reading and any feedback is welcome and appreciated. biorxiv.org/content/10.110… We present a novel metagenomic profiling tool, KMCP, which not only allows for accurate taxonomic profiling of archaea, bacteria, and viral populations from metagenomic shotgun sequence data, but also provides confident pathogen detection for clinical samples of low depth.