Efficient computation of contributional diversity metrics from microbiome data with FuncDiv.
Bioinformatics
; 39(1)2023 01 01.
Article
en En
| MEDLINE
| ID: mdl-36519836
ABSTRACT
MOTIVATION Microbiome datasets with taxa linked to the functions (e.g. genes) they encode are becoming more common as metagenomics sequencing approaches improve. However, these data are challenging to analyze due to their complexity. Summary metrics, such as the alpha and beta diversity of taxa contributing to each function (i.e. contributional diversity), represent one approach to investigate these data, but currently there are no straightforward methods for doing so. RESULTS:
We addressed this gap by developing FuncDiv, which efficiently performs these computations. Contributional diversity metrics can provide novel insights that would be impossible to identify without jointly considering taxa and functions. AVAILABILITY AND IMPLEMENTATION FuncDiv is distributed under a GNU Affero General Public License v3.0 and is available at https//github.com/gavinmdouglas/FuncDiv. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Microbiota
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2023
Tipo del documento:
Article
País de afiliación:
Canadá