High‐throughput sequencing (HTS) is central to the study of population genomics and has an increasingly important role in constructing phylogenies. Choices in research design for sequencing projects can include a wide range of factors, such as sequencing platform, depth of coverage and bioinformatic tools. Simulating HTS data better informs these decisions, as users can validate software by comparing output to the known simulation parameters. However, current standalone HTS simulators cannot generate variant haplotypes under even somewhat complex evolutionary scenarios, such as recombination or demographic change. This greatly reduces their usefulness for fields such as population genomics and phylogenomics. Here I present the R package jackalope that simply and efficiently simulates (i) sets of variant haplotypes from a reference genome and (ii) reads from both Illumina and Pacific Biosciences platforms. Haplotypes can be simulated using phylogenies, gene trees, coalescent‐simulation output, population‐genomic summary statistics, and Variant Call Format (VCF) files. jackalope can simulate single, paired‐end or mate‐pair Illumina reads, as well as reads from Pacific Biosciences. These simulations include sequencing errors, mapping qualities, multiplexing and optical/PCR duplicates. It can read reference genomes from fasta files and can simulate new ones, and all outputs can be written to standard file formats. jackalope is available for Mac, Windows and Linux systems.

中文翻译：

---

jackalope：快速，通用的系统生物学和高通量测序模拟器。

高通量测序（HTS）对种群基因组学的研究至关重要，并且在构建系统发育上起着越来越重要的作用。测序项目的研究设计选择可能包括多种因素，例如测序平台，覆盖范围和生物信息学工具。仿真HTS数据可以更好地指导这些决策，因为用户可以通过将输出与已知仿真参数进行比较来验证软件。但是，当前的独立HTS模拟器即使在较为复杂的进化方案（例如重组或人口变化）下也无法生成变​​异单倍型。这大大降低了其在诸如种群基因组学和系统发育组学等领域的有用性。在这里，我介绍了R包jackalope可以简单，有效地模拟（i）参考基因组的变异单倍体组，以及（ii）从Illumina和Pacific Biosciences平台读取数据。可以使用系统发育树，基因树，合并模拟输出，群体基因组摘要统计和变异调用格式（VCF）文件来模拟单倍型。jackalope可以模拟Illumina的单个，成对末端或配对配对的读数，以及来自Pacific Biosciences的读数。这些模拟包括测序错误，作图质量，多路复用和光学/ PCR重复。它可以从fasta文件中读取参考基因组，并可以模拟新的基因组，并且所有输出都可以写入标准文件格式。jackalope可用于Mac，Windows和Linux系统。