Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq.
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ABSTRACT:
SUBMITTER: Deatherage DE
PROVIDER: S-EPMC4239701 | biostudies-literature | 2014
REPOSITORIES: biostudies-literature
Publications
Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq.
Deatherage Daniel E DE Barrick Jeffrey E JE
Methods in molecular biology (Clifton, N.J.) 20140101
Next-generation DNA sequencing (NGS) can be used to reconstruct eco-evolutionary population dynamics and to identify the genetic basis of adaptation in laboratory evolution experiments. Here, we describe how to run the open-source breseq computational pipeline to identify and annotate genetic differences found in whole-genome and whole-population NGS data from haploid microbes where a high-quality reference genome is available. These methods can also be used to analyze mutants isolated in geneti ...[more]
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