Computational analyses of bacterial strains from shotgun reads.
Brief Bioinform
; 23(2)2022 03 10.
Article
in En
| MEDLINE
| ID: mdl-35136954
ABSTRACT
Shotgun sequencing is routinely employed to study bacteria in microbial communities. With the vast amount of shotgun sequencing reads generated in a metagenomic project, it is crucial to determine the microbial composition at the strain level. This study investigated 20 computational tools that attempt to infer bacterial strain genomes from shotgun reads. For the first time, we discussed the methodology behind these tools. We also systematically evaluated six novel-strain-targeting tools on the same datasets and found that BHap, mixtureS and StrainFinder performed better than other tools. Because the performance of the best tools is still suboptimal, we discussed future directions that may address the limitations.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Metagenomics
/
Microbiota
Language:
En
Journal:
Brief Bioinform
Journal subject:
BIOLOGIA
/
INFORMATICA MEDICA
Year:
2022
Type:
Article
Affiliation country:
United States