Efficient inference of large prokaryotic pangenomes with PanTA

Autor: Duc Quang Le, Tien Anh Nguyen, Son Hoang Nguyen, Tam Thi Nguyen, Canh Hao Nguyen, Huong Thanh Phung, Tho Huu Ho, Nam S. Vo, Trang Nguyen, Hoang Anh Nguyen, Minh Duc Cao
Jazyk: angličtina
Rok vydání: 2024
Předmět:
Zdroj: Genome Biology, Vol 25, Iss 1, Pp 1-16 (2024)
Druh dokumentu: article
ISSN: 1474-760X
DOI: 10.1186/s13059-024-03362-z
Popis: Abstract Pangenome inference is an indispensable step in bacterial genomics, yet its scalability poses a challenge due to the rapid growth of genomic collections. This paper presents PanTA, a software package designed for constructing pangenomes of large bacterial datasets, showing unprecedented efficiency levels multiple times higher than existing tools. PanTA introduces a novel mechanism to construct the pangenome progressively without rebuilding the accumulated collection from scratch. The progressive mode is shown to consume orders of magnitude less computational resources than existing solutions in managing growing datasets. The software is open source and is publicly available at https://github.com/amromics/panta and at 10.6084/m9.figshare.23724705 .
Databáze: Directory of Open Access Journals