LMAS: evaluating metagenomic short de novo assembly methods through defined communities.

ABSTRACT:

Background

The de novo assembly of raw sequence data is key in metagenomic analysis. It allows recovering draft genomes from a pool of mixed raw reads, yielding longer sequences that offer contextual information and provide a more complete picture of the microbial community.

Findings

To better compare de novo assemblers for metagenomic analysis, LMAS (Last Metagenomic Assembler Standing) was developed as a flexible platform allowing users to evaluate assembler performance given known standard communities. Overall, in our test datasets, k-mer De Bruijn graph assemblers outperformed the alternative approaches but came with a greater computational cost. Furthermore, assemblers branded as metagenomic specific did not consistently outperform other genomic assemblers in metagenomi

SUBMITTER: Mendes CI 

PROVIDER: S-EPMC9795473 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature