Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies.

ABSTRACT:

Background

In the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing coverage. This conjuncture is rarely tested or evaluated in practice. We often do not know how many abundant species are missing and do not have an approach to recover them.

Results

Here, we propose k-mer based and 16S RNA based methods to measure the completeness of metagenome assembly. We show that even with PacBio high-fidelity (HiFi) reads, abundant species are often not assembled, as high strain diversity may lead to fragmented contigs. We develop a novel reference-free algorithm to recover abundant metagenome-assembled genomes (MAGs) by identifying circular assembly subgraphs. Complemented with a reference-free genome binnin

SUBMITTER: Feng X 

PROVIDER: S-EPMC11007910 | biostudies-literature | 2024 Apr

REPOSITORIES: biostudies-literature