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barricklab / breseq

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.
http://barricklab.org/breseq
GNU General Public License v2.0
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bowtie2 versions #373

Closed gabypetrungaro closed 3 weeks ago

gabypetrungaro commented 3 weeks ago

Hi, when running breseq 0.38.2, I get a warning about the bowtie2 version (see below). However, apparently the recommended version of bowtie2 (2.4.5) is older that the one it is using (version 2.5.3), right?. Why would breseq recommend to use an older version of bowtie2?

Thanks and best, Gabriela.

================================================================================ breseq 0.38.2 http://barricklab.org/breseq

Active Developers: Barrick JE, Deatherage DE Contact: jeffrey.e.barrick@gmail.com

breseq is free software; you can redistribute it and/or modify it under the terms the GNU General Public License as published by the Free Software Foundation; either version 2, or (at your option) any later version.

Copyright (c) 2008-2010 Michigan State University Copyright (c) 2011-2022 The University of Texas at Austin

If you use breseq in your research, please cite:

Deatherage, D.E., Barrick, J.E. (2014) Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151: 165–188.

If you use structural variation (junction) predictions, please cite:

Barrick, J.E., Colburn, G., Deatherage D.E., Traverse, C.C., Strand, M.D., Borges, J.J., Knoester, D.B., Reba, A., Meyer, A.G. (2014) Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC Genomics 15:1039.

---> bowtie2 :: version 2.5.3 [/home/gpetrung/conda_env_breseq038/bin/bowtie2] ---> bowtie2 :: NOTE :: breseq output may vary slightly depending on your bowtie2 version ---> bowtie2 :: NOTE :: and occasionally bowtie2 versions may have bugs that cause crashes. ---> bowtie2 :: NOTE :: bowtie2 version 2.4.5 is recommended with this breseq version. ---> R :: version 4.3.2 [/home/gpetrung/conda_env_breseq038/bin/R]

jeffreybarrick commented 3 weeks ago

Most likely newer bowtie2 versions are fine.

Version 2.5.3 is suggested because it's been tested with breseq and occasionally updates introduce bugs or changes in programs that disrupt compatibility.

gabypetrungaro commented 3 weeks ago

thanks, version 2.5.3 is the one used (suggested was 2.4.5, thus the question)