breseq pipeline

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



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Publication for breseq

breseq citations

PMCID: 3576414

[…] point samples using both the main public server and local instances of galaxy (details below) [54]–[56]. to identify larger indels and estimate their frequencies in the time point samples, we used breseq version 0.16 [57]. the sequence [58] of the ancestral strain rel606 (genbank accession number nc_012967.1) was used as the reference for all mutation screens., fastq files were first filtered […]

PMCID: 3542559

[…] genome was obtained from a single colony of a corpus-derived population, ciii-1org, isolated at t0 (schott et al. 2011). polymorphisms were predicted by applying the model implemented in the breseq pipeline that allowed the population to be, in each position, an arbitrary mixture of the two most frequent bases. only polymorphisms where both bases were predicted to be present […]

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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