breseq statistics

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Citations per year

Number of citations per year for the bioinformatics software tool breseq

Tool usage distribution map

This map represents all the scientific publications referring to breseq per scientific context
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Associated diseases


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breseq specifications


Unique identifier OMICS_00298
Name breseq
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available

Publication for breseq

breseq citations


Clinically Relevant Plasmid Host Interactions Indicate that Transcriptional and Not Genomic Modifications Ameliorate Fitness Costs of Klebsiella pneumoniae Carbapenemase Carrying Plasmids

PMCID: 5915730
PMID: 29691332
DOI: 10.1128/mBio.02303-17
call_split See protocol

[…] rains were performed using SPAdes with the –careful flag and were annotated using Prokka. Raw sequence data of plasmid-containing strains were aligned to the sequence of the plasmid-free parent using Breseq, with reads mapped against each individual contig of the de novo assembly to avoid issues associated with contig breaks. In order to look for SNPs and indels between the plasmid DNA sequences o […]


Innovation in an E. coli evolution experiment is contingent on maintaining adaptive potential until competition subsides

PLoS Genet
PMCID: 5918244
PMID: 29649242
DOI: 10.1371/journal.pgen.1007348
call_split See protocol

[…] ilable via links from the main LTEE NCBI BioProject page (PRJNA414462).We initially predicted mutations in each re-sequenced genome by comparing Illumina reads to the REL606 reference genome [] using breseq (v0.31.1) [,]. Then, we further curated the lists of predicted mutations as previously described []. Briefly, a maximum-parsimony phylogenetic tree for all 61 strains from the LTEE population w […]


Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population based study

PLoS One
PMCID: 5884559
PMID: 29617456
DOI: 10.1371/journal.pone.0195413

[…] excluding genetic regions annotated as PE/PPE, PGRS, pks, esx, repeat, polyketide, or transposase in the gene name and/or gene product description in the annotated Genome Difference files produced by Breseq. Isolates with a maximum pair-wise distance of 12 SNPs in the proportion of the genome analysed, were assigned to a WGS cluster, as suggested earlier by Walker et al., 2013 []. We investigated […]


Experimental evolution of diverse Escherichia coli metabolic mutants identifies genetic loci for convergent adaptation of growth rate

PLoS Genet
PMCID: 5892946
PMID: 29584733
DOI: 10.1371/journal.pgen.1007284

[…] m each strain was assembled to the E. coli BW25113 WT genome template [], and polymorphisms were identified using Geneious v 7.1.4 []. Additionally, we reanalyzed our genome sequencing data using the breseq analysis pipeline to account for possible IS element insertions []. Breseq confirmed the single nucleotide polymorphisms (SNPs) and small insertion/deletions identified by Geneious, and reveale […]


Physiological Effect of XoxG(4) on Lanthanide Dependent Methanotrophy

PMCID: 5874918
PMID: 29588409
DOI: 10.1128/mBio.02430-17

[…] is, including single nucleotide polymorphisms (SNP) and indels. The mapped reads were also processed with breseq (0.31.1). Finally, variant results were summarized and filtered by GATK, Samtools, and breseq. […]


Population Genomics of Francisella tularensis subsp. holarctica and its Implication on the Eco Epidemiology of Tularemia in Switzerland

PMCID: 5875085
PMID: 29623260
DOI: 10.3389/fcimb.2018.00089

[…] Breseq analysis revealed 259 polymorphisms within the 59 sequenced Fth genomes relative to the genome FTNF002-00. We identified 36 deletions, 28 insertions and 195 SNPs. Seventy-nine SNPs were non-syn […]

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breseq institution(s)
Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, USA

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