SEQ2MGS: an effective tool for generating realistic artificial metagenomes from the existing sequencing data.

ABSTRACT: Assessment of bioinformatics tools for the metagenomics analysis from the whole genome sequencing data requires realistic benchmark sets. We developed an effective and simple generator of artificial metagenomes from real sequencing experiments. The tool (SEQ2MGS) analyzes the input FASTQ files, precomputes genomic content, and blends shotgun reads from different sequenced isolates, or spike isolate(s) in real metagenome, in desired proportions. SEQ2MGS eliminates the need for simulation of sequencing platform variations, reads distributions, presence of plasmids, viruses, and contamination. The tool is especially useful for a quick generation of multiple complex samples that include new or understudied organisms, even without assembled genomes. For illustration, we first demonstrated the e

SUBMITTER: Van Camp PJ 

PROVIDER: S-EPMC9310082 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature