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

Abstract

A growing number of microbial reference genomes enable better metagenomic profiling accuracy yet put higher requirements on the indexing efficiency, database size, and runtime of taxonomic profilers. Besides, most profilers focused mainly on bacterial, archaeal, and fungal populations with less attention on viral communities. We present KMCP, a novel k-mer based metagenomic profiling tool that introduces genomic positions to k-mers by splitting the reference genomes into chunks. Benchmarking results on both simulated and real data demonstrate that KMCP 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 infectious clinical samples of low depth. KMCP is implemented in Go and is available as open-source software, under MIT, at https://github.com/shenwei356/kmcp.

Phanta: Phage-inclusive profiling of human gut metagenomes

“…Shotgun metagenomics is a popular and affordable method to sequence metagenomic samples [10][11][12][13] . This method captures genomic DNA from all gut organisms, not only prokaryotes, making it an optimal tool to study DNA viruses of the virome [14][15][16] . In the past decade, thousands of human microbiome samples have been analyzed using this "domain-inclusive" method [17][18][19][20] .…”