breseq protocols

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breseq specifications

Information


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

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Publication for breseq

breseq in pipelines

 (11)
2017
PMCID: 5310122
PMID: 28196526
DOI: 10.1186/s12864-017-3572-2

[…] standard protocols. the whole-genome sequences are deposited in the sequence read archive (sra) database (http://www.ncbi.nlm.nih.gov/sra/) and are available with access number srp048919. breseq (v0.27.1) [] pipeline was used to first align the reads of the reference s288c genome (using bowtie2 [], and to identify snps and indels with a frequency cutoff of 0.2. cnv detection […]

2017
PMCID: 5395140
PMID: 28419091
DOI: 10.1371/journal.pbio.2001741

[…] in the rifr pool, 640x for 12 clones in the strr pool, and 631x for 24 clones in the rifr strr pool. the reads were filtered using seqtk version 1.0-r63. the resulting sequences were analyzed in breseq version 2.3, using e. coli k12 genome nc_000913.2 as a reference, and with the polymorphism option selected and the following parameters: (a) rejection of polymorphisms in homopolymers […]

2017
PMCID: 5465629
PMID: 28596410
DOI: 10.1128/genomeA.00493-17

[…] miseq at the university of minnesota genomics center (minneapolis, mn). paired-end short-read data (2 × 250 bp) with at least 100× coverage were mapped to the long-read assembly reference using breseq (), and single-nucleotide polymorphisms (snps)/indels were corrected with pilon () to yield high-quality genome sequences. sequences of large linear chromosomes assembled to a single contig […]

2017
PMCID: 5472167
PMID: 28593940
DOI: 10.1038/ncomms15589

[…] were aligned to the mg1655 reference data (nc_000913.2). alignment was performed using bowtie2. snps and indels were identified using samtools. identification of mutations were analysed using breseq (ref. ). a minimum coverage of 100-fold was accomplished with each strain. selected putative variants (snps and indels) detected by whole-genome resequencing were verified by pcr followed […]

2016
PMCID: 4827201
PMID: 27069508
DOI: 10.1186/s13068-016-0497-y

[…] changes between the sequenced strain and the butanol tolerant strains, the results of three independent analyses were combined. first, the raw reads were aligned to the genome and processed using breseq version 0.19 []. next, the raw reads were quality filtered using nesoni version 0.122 (nesoni 2014). the filtered reads were assembled using spades version 3.0 []. the assembled contigs […]


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breseq in publications

 (134)
PMCID: 5942850
PMID: 29702649
DOI: 10.1371/journal.pgen.1007324

[…] of the genome. in virtually all sequenced samples less than 1% of the genome had no sequence coverage (). we identified the frequency of snps in each sequenced population and their annotations using breseq, which has been widely used in microbial studies and has been optimized for bacterial data [] (). we discovered several snps at non-zero frequency in these sequenced ancestral populations (1, […]

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

[…] 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 […]

PMCID: 5918244
PMID: 29649242
DOI: 10.1371/journal.pgen.1007348

[…] 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 […]

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

[…] the pykf [], rpob and rpoc [, ] loci are consistent with other studies of e. coli in minimal medium, and are directly associated with faster growth (). analysis of the dna sequencing data using the breseq package [] demonstrated that mutations in pykf were a consequence of is5 insertions, transition mutations, and single base deletions. rpob and rpoc mutations were a result of both transition […]

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

[…] (v2.3.0). the mapped data were called by gatk (v3.7) and samtools (v1.4) for variant analysis, 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., rna was extracted from the wild-type strain culture and from δxoxg mutant culture […]


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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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