The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. Inferring the core genome is integral to many genomic analyses, however, most methods rely on the comparison of all the pairs of genomes; a step that is becoming increasingly difficult given the massive accumulation of genomic data. Here, we present CoreCruncher; a program that robustly and rapidly constructs core genomes across hundreds or thousands of genomes. CoreCruncher does not compute all pairwise genome comparisons and uses a heuristic based on the distributions of identity scores to classify sequences as orthologs or paralogs/xenologs. Although it is much faster than current methods, our results indicate that our approach is more conservative than other tools and less sensitive to the presence of paralogs and xenologs. CoreCruncher is freely available at https://github.com/lbobay/CoreCruncher. CoreCruncher is written in Python 3.7 but can also run on Python 2.7 without modification. It requires the python library Numpy and either Usearch or Blast. Certain options require the programs muscle or mafft.

中文翻译：

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CoreCruncher：在大型原核数据集中快速，强大地构建核心基因组。

核心基因组代表给定种群或原核生物种的所有或几乎所有菌株共有的一组基因。推断核心基因组是许多基因组分析必不可少的，但是，大多数方法都依赖于所有基因组对的比较。鉴于基因组数据的大量积累，这一步骤变得越来越困难。在这里，我们介绍CoreCruncher；该程序可以快速，强大地构建数百或数千个基因组的核心基因组。CoreCruncher并不计算所有成对的基因组比较，而是使用基于同一性得分分布的启发式方法将序列分类为直系同源物或旁系同源物/异种同源物。尽管它比当前方法快得多，但是我们的结果表明，我们的方法比其他工具更为保守，并且对旁系同源物和异种同源物的存在较不敏感。可在https://github.com/lbobay/CoreCruncher上免费获得CoreCruncher。CoreCruncher用Python 3.7编写，但也可以在Python 2.7上运行而无需修改。它需要python库Numpy和Usearch或Blast。某些选项的节目肌肉或MAFFT。