mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes.
Bioinformatics
; 38(1): 270-272, 2021 12 22.
Article
em En
| MEDLINE
| ID: mdl-34260698
ABSTRACT
Profiling the taxonomic composition of microbial communities commonly involves the classification of ribosomal RNA gene fragments. As a trade-off to maintain high classification accuracy, existing tools are typically limited to the genus level. Here, we present mTAGs, a taxonomic profiling tool that implements the alignment of metagenomic sequencing reads to degenerate consensus reference sequences of small subunit ribosomal RNA genes. It uses DNA fragments, that is, paired-end sequencing reads, as count units and provides relative abundance profiles at multiple taxonomic ranks, including operational taxonomic units based on a 97% sequence identity cutoff. At the genus rank, mTAGs outperformed other tools across several metrics, such as the F1 score by >11% across data from different environments, and achieved competitive (F1 score) or better results (Bray-Curtis dissimilarity) at the sub-genus level. AVAILABILITY AND IMPLEMENTATION The software tool mTAGs is implemented in Python. The source code and binaries are freely available (https//github.com/SushiLab/mTAGs). The data underlying this article are available in Zenodo, at https//doi.org/10.5281/zenodo.4352762. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Microbiota
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2021
Tipo de documento:
Article
País de afiliação:
Suíça