Identification of Mutations in Laboratory-Evolved Microbes from Next-Generation Sequencing Data Using breseq
DE Deatherage, JE Barrick - Engineering and analyzing multicellular …, 2014 - Springer
DE Deatherage, JE Barrick
Engineering and analyzing multicellular systems: methods and protocols, 2014•SpringerNext-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 genetic screens and to detect …
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 genetic screens and to detect …
Abstract
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 genetic screens and to detect unintended mutations that may occur during strain construction and genome editing.
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