GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences

BMC Bioinformatics
Migle Gabrielaite, Rasmus L Marvig

Abstract

Bacterial gene loss and acquisition is a well-known phenomenon which contributes to bacterial adaptation through changes in important phenotypes such as virulence, antibiotic resistance and metabolic capability. While advances in DNA sequencing have accelerated our ability to generate short genome sequence reads to disentangle phenotypic changes caused by gene loss and acquisition, the short-read genome sequencing often results in fragmented genome assemblies as a basis for identification of gene loss and acquisition events. However, sensitive and precise determination of gene content change for fragmented genome assemblies remains challenging as analysis needs to account for cases when only a fragment of the gene is assembled or when the gene assembly is split in more than one contig. We developed GenAPI, a command-line tool that is designed to compare the gene content of bacterial genomes for which only fragmented genome assemblies are available. GenAPI, unlike other available tools of similar purpose, accounts for imperfections in sequencing and assembly, and aims to compensate for them. We tested the performance of GenAPI on three different datasets to show that GenAPI has a high sensitivity while it maintains precision whe...Continue Reading

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Citations

Jan 22, 2021·Journal of Clinical Microbiology·Migle GabrielaiteRasmus L Marvig
Jul 8, 2021·Microbial Genomics·Migle GabrielaiteRasmus L Marvig

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Software Mentioned

Bedtools
BPGA
EDGAR
pheatmap
CD
GenAPI
HIT
Roary
SPAdes
panX

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