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金洁琼, 孙艳波. 2018: AutoSeqMan:用于组装第一代测序数据的自动化工具. 动物学研究, 39(2): 123-126. DOI: 10.24272/j.issn.2095-8137.2018.027
引用本文: 金洁琼, 孙艳波. 2018: AutoSeqMan:用于组装第一代测序数据的自动化工具. 动物学研究, 39(2): 123-126. DOI: 10.24272/j.issn.2095-8137.2018.027
Jie-Qiong Jin, Yan-Bo Sun. 2018: AutoSeqMan: batch assembly of contigs for Sanger sequences. Zoological Research, 39(2): 123-126. DOI: 10.24272/j.issn.2095-8137.2018.027
Citation: Jie-Qiong Jin, Yan-Bo Sun. 2018: AutoSeqMan: batch assembly of contigs for Sanger sequences. Zoological Research, 39(2): 123-126. DOI: 10.24272/j.issn.2095-8137.2018.027

AutoSeqMan:用于组装第一代测序数据的自动化工具

AutoSeqMan: batch assembly of contigs for Sanger sequences

  • 摘要: 尽管高通量测序技术已得到广泛应用,目前仍有许多研究领域需要第一代测序技术(Sanger测序)产生的序列数据,譬如进化分类学等。SeqMan(Lasergene软件包)是一款优秀的组装Sanger序列的图形用户界面程序(GUI)。然而,随着数据规模越来越大(如样本数、基因数),科研人员需要执行大量的手工操作以分类、组装这些数据。因此,设计一款能够自动化处理这些数据的工具变得越来越有必要。基于此,我们开发了autoSeqMan,它主要包括两个功能模块,即“分类”和“组装”。“分类”模块首先对原始数据进行预处理、编组;“组装”模块随后对处理过的数据生成批处理脚本(SeqMan脚本编程语言)并自动运行SeqMan(需要用户提前安装)。通过与手工操作比较,我们发现autoSeqMan在序列数据的预处理和组装上均节省大量时间。我们希望该工具能够为那些有大样本集分析需求的科研人员提供帮助。该工具可在https://github.com/sun-yanbo/autoseqman免费下载安装。

     

    Abstract: With the wide application of DNA sequencing technology, DNA sequences are still increasingly generated through the Sanger sequencing platform. SeqMan (in the LaserGene package) is an excellent program with an easy-to-use graphical user interface (GUI) employed to assemble Sanger sequences into contigs. However, with increasing data size, larger sample sets and more sequenced loci make contig assemble complicated due to the considerable number of manual operations required to run SeqMan. Here, we present the ‘autoSeqMan’ software program, which can automatedly assemble contigs using SeqMan scripting language. There are two main modules available, namely, ‘Classification’ and ‘Assembly’. Classification first undertakes preprocessing work, whereas Assembly generates a SeqMan script to consecutively assemble contigs for the classified files. Through comparison with manual operation, we showed that autoSeqMan saved substantial time in the preprocessing and assembly of Sanger sequences. We hope this tool will be useful for those with large sample sets to analyze, but with little programming experience. It is freely available at https://github.com/ Sun-Yanbo/autoSeqMan.

     

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