Cognac: Rapid Generation of Concatenated Gene Alignments for Phylogenetic Inference from Large, Bacterial Whole Genome Sequencing Datasets

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2021 Feb 16

PMID 33588753

Citations 6

Authors

Ryan D Crawford

Evan S Snitkin

Affiliations

Soon will be listed here.

Abstract

Background: The quantity of genomic data is expanding at an increasing rate. Tools for phylogenetic analysis which scale to the quantity of available data are required. To address this need, we present cognac, a user-friendly software package to rapidly generate concatenated gene alignments for phylogenetic analysis.

Results: We illustrate that cognac is able to rapidly identify phylogenetic marker genes using a data driven approach and efficiently generate concatenated gene alignments for very large genomic datasets. To benchmark our tool, we generated core gene alignments for eight unique genera of bacteria, including a dataset of over 11,000 genomes from the genus Escherichia producing an alignment with 1353 genes, which was constructed in less than 17 h.

Conclusions: We demonstrate that cognac presents an efficient method for generating concatenated gene alignments for phylogenetic analysis. We have released cognac as an R package ( https://github.com/rdcrawford/cognac ) with customizable parameters for adaptation to diverse applications.

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