Maast: genotyping thousands of microbial strains efficiently.
Genome Biol
; 24(1): 186, 2023 08 10.
Article
in En
| MEDLINE
| ID: mdl-37563669
ABSTRACT
Existing single nucleotide polymorphism (SNP) genotyping algorithms do not scale for species with thousands of sequenced strains, nor do they account for conspecific redundancy. Here we present a bioinformatics tool, Maast, which empowers population genetic meta-analysis of microbes at an unrivaled scale. Maast implements a novel algorithm to heuristically identify a minimal set of diverse conspecific genomes, then constructs a reliable SNP panel for each species, and enables rapid and accurate genotyping using a hybrid of whole-genome alignment and k-mer exact matching. We demonstrate Maast's utility by genotyping thousands of Helicobacter pylori strains and tracking SARS-CoV-2 diversification.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
SARS-CoV-2
/
COVID-19
Type of study:
Systematic_reviews
Limits:
Humans
Language:
En
Journal:
Genome Biol
Journal subject:
BIOLOGIA MOLECULAR
/
GENETICA
Year:
2023
Type:
Article
Affiliation country:
United States