Producing polished prokaryotic pangenomes with the Panaroo pipeline
Producing polished prokaryotic pangenomes with the Panaroo pipeline
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DOI：
10.1186/s13059-020-02090-4
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发表时间：
2020-07-22
期刊：
影响因子：
12.3
通讯作者：
Parkhill, Julian
中科院分区：
文献类型：
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作者：
Tonkin-Hill, Gerry;MacAlasdair, Neil;Parkhill, Julian
原核生物基因组的种群水平比较必须考虑到水平基因转移、基因复制和基因丢失导致的基因含量的显著差异。然而，原核生物基因组的自动注释是不完善的，由于碎片组装、污染、多样化的基因家族和错误组装而导致的错误在种群中积累，导致在分析一个物种中发现的所有基因集时产生深远的后果。在这里，我们介绍Panaroo，一个基于图形的Pangenome聚类工具，它能够解释原核生物基因组组装注释过程中引入的许多错误来源。Panaroo在https://github.com/gtonkinhill/panaroo.上有售
Population-level comparisons of prokaryotic genomes must take into account the substantial differences in gene content resulting from horizontal gene transfer, gene duplication and gene loss. However, the automated annotation of prokaryotic genomes is imperfect, and errors due to fragmented assemblies, contamination, diverse gene families and mis-assemblies accumulate over the population, leading to profound consequences when analysing the set of all genes found in a species. Here, we introduce Panaroo, a graph-based pangenome clustering tool that is able to account for many of the sources of error introduced during the annotation of prokaryotic genome assemblies. Panaroo is available at https://github.com/gtonkinhill/panaroo.