Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq.
Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq.
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DOI：
10.1007/978-1-4939-0554-6_12
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发表时间：
2014
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下一代DNA测序（NGS）可用于重建生态进化种群动态，并在实验室进化实验中确定适应性的遗传基础。在此，我们描述如何运行开源的breseq计算流程，以识别和注释在单倍体微生物的全基因组和全种群NGS数据中发现的遗传差异，前提是有高质量的参考基因组可用。这些方法还可用于分析在遗传筛选中分离出的突变体，并检测在菌株构建和基因组编辑过程中可能出现的非预期突变。
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.