Decreasing sequencing costs have driven a rapid expansion of novel genotyping methods. One of these methods is the exploitation of restriction enzyme cut sites to generate genome-wide but reduced representation sequencing libraries (RRLs), alternatively termed genotyping by sequencing or restriction-site associated DNA sequencing. Without a reference genome, the resulting short sequence reads must be assembled de novo. There are many possible assembly programs, most not explicitly developed for RRL data, and we know little of their effectiveness. In this issue of Molecular Ecology Resources, LaCava et al. (2020) systematically evaluate six commonly used programs and two commonly varied parameters for complete and accurate assembly of RRLs, using simulated double digests of Homo sapiens and Arabidopsis thaliana genomes with varied mutation rates and types. The authors find substantial variation in performance across assembly programs. The most consistently high-performing assembler is infrequently used in their literature survey (CD-HIT; Li and Godzik, 2006), while several others fail to produce complete, accurate assemblies under many conditions. LaCava et al. additionally recommend best practices in parameter choice and evaluation of future assembly programs-advice that molecular ecologists working to assemble sequences of all kinds should take to heart.

中文翻译：

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堆叠RADSeq组装程序：从完全打击到完全糟糕。

测序成本的降低推动了新型基因分型方法的迅速发展。这些方法之一是利用限制酶切割位点来生成全基因组但减少的代表性测序文库（RRL），也称为通过测序或限制性位点相关的DNA测序进行基因分型。如果没有参考基因组，则必须从头组装所得的短序列读数。有很多可能的汇编程序，其中大多数没有为RRL数据明确开发，我们对其效果知之甚少。在本期《分子生态资源》中，LaCava等人。（2020年）系统地评估六个常用程序和两个常用变化参数，以完整而准确地组装RRL，使用智人和拟南芥基因组的模拟双消化物，其突变率和类型各不相同。作者发现整个汇编程序的性能存在很大差异。在他们的文献调查中，很少会使用性能最高的组装机（CD-HIT； Li和Godzik，2006），而其他几种组装机在许多情况下都无法生产完整，准确的组装机。LaCava等。此外，还建议在参数选择和将来的组装程序评估中推荐最佳实践，这是分子生态学家努力组装各种序列的建议。而其他几个在许多情况下都无法生产出完整，准确的组件。LaCava等。此外，还建议在参数选择和将来的组装程序评估中推荐最佳实践，这是分子生态学家努力组装各种序列的建议。而其他几个在许多情况下都无法生产出完整，准确的组件。LaCava等。此外，还建议在参数选择和将来的组装程序评估中推荐最佳实践，这是分子生态学家努力组装各种序列的建议。