Ryan D Crawford1, Evan S Snitkin2. 1. Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA. 2. Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA. esnitkin@umich.edu.
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.
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.
Authors: M C Maiden; J A Bygraves; E Feil; G Morelli; J E Russell; R Urwin; Q Zhang; J Zhou; K Zurth; D A Caugant; I M Feavers; M Achtman; B G Spratt Journal: Proc Natl Acad Sci U S A Date: 1998-03-17 Impact factor: 11.205
Authors: Stephen J Bush; Dona Foster; David W Eyre; Emily L Clark; Nicola De Maio; Liam P Shaw; Nicole Stoesser; Tim E A Peto; Derrick W Crook; A Sarah Walker Journal: Gigascience Date: 2020-02-01 Impact factor: 6.524
Authors: Ramy K Aziz; Daniela Bartels; Aaron A Best; Matthew DeJongh; Terrence Disz; Robert A Edwards; Kevin Formsma; Svetlana Gerdes; Elizabeth M Glass; Michael Kubal; Folker Meyer; Gary J Olsen; Robert Olson; Andrei L Osterman; Ross A Overbeek; Leslie K McNeil; Daniel Paarmann; Tobias Paczian; Bruce Parrello; Gordon D Pusch; Claudia Reich; Rick Stevens; Olga Vassieva; Veronika Vonstein; Andreas Wilke; Olga Zagnitko Journal: BMC Genomics Date: 2008-02-08 Impact factor: 3.969
Authors: Jay Vornhagen; Emily K Roberts; Lavinia Unverdorben; Sophia Mason; Alieysa Patel; Ryan Crawford; Caitlyn L Holmes; Yuang Sun; Alexandra Teodorescu; Evan S Snitkin; Lili Zhao; Patricia J Simner; Pranita D Tamma; Krishna Rao; Keith S Kaye; Michael A Bachman Journal: Nat Commun Date: 2022-08-01 Impact factor: 17.694
Authors: Zena Lapp; Ryan Crawford; Arianna Miles-Jay; Ali Pirani; William E Trick; Robert A Weinstein; Mary K Hayden; Evan S Snitkin; Michael Y Lin Journal: Clin Infect Dis Date: 2021-10-20 Impact factor: 9.079
Authors: Sarah E Sansom; Emily Benedict; Stephanie N Thiede; Bala Hota; Alla Aroutcheva; Darjai Payne; Chad Zawitz; Evan S Snitkin; Stefan J Green; Robert A Weinstein; Kyle J Popovich Journal: Microbiol Spectr Date: 2021-07-21