RT Journal Article
SR Electronic
T1 Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.01.15.426834
DO 10.1101/2021.01.15.426834
A1 Pengfan Zhang
A1 Stjin Spaepen
A1 Yang Bai
A1 Stephane Hacquard
A1 Ruben Garrido-Oter
YR 2021
UL http://biorxiv.org/content/early/2021/03/10/2021.01.15.426834.abstract
AB Summary Synthetic microbial communities (SynComs) constitute an emerging and powerful tool in biological, biomedical, and biotechnological research. Despite recent advances in algorithms for the analysis of culture-independent amplicon sequencing data from microbial communities, there is a lack of tools specifically designed for analysing SynCom data, where reference sequences for each strain are available. Here we present Rbec, a tool designed for the analysis of SynCom data that accurately corrects PCR and sequencing errors in amplicon sequences and identifies intra-strain polymorphic variation. Extensive evaluation using mock bacterial and fungal communities show that our tool outperforms current methods for samples of varying complexity, diversity, and sequencing depth. Furthermore, Rbec also allows accurate detection of contaminants in SynCom experiments.Availability and implementation Rbec is freely available as an open-source multi-platform R package. Release versions can be obtained via Bioconductor. The developer version is maintained and can be downloaded at: https://github.com/PengfanZhang/Rbec.Contact garridoo{at}mpipz.mpg.deCompeting Interest StatementThe authors have declared no competing interest.