KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping.

ABSTRACT:

Motivation

The growing number of microbial reference genomes enables the improvement of metagenomic profiling accuracy but also imposes greater requirements on the indexing efficiency, database size and runtime of taxonomic profilers. Additionally, most profilers focus mainly on bacterial, archaeal and fungal populations, while less attention is paid to viral communities.

Results

We present KMCP (K-mer-based Metagenomic Classification and Profiling), a novel k-mer-based metagenomic profiling tool that utilizes genome coverage information by splitting the reference genomes into chunks and stores k-mers in a modified and optimized Compact Bit-Sliced Signature Index for fast alignment-free sequence searching. KMCP combines k-mer similarity and genome coverage information to red

SUBMITTER: Shen W 

PROVIDER: S-EPMC9828150 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature