Please wait a minute...
Zoological Research    2018, Vol. 39 Issue (2) : 123-126     DOI: 10.24272/j.issn.2095-8137.2018.027
Reports |
AutoSeqMan: batch assembly of contigs for Sanger sequences
Jie-Qiong Jin1, Yan-Bo Sun1,*
1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
Download: PDF(1275 KB)   RICH HTML
Export: BibTeX | EndNote | Reference Manager | ProCite | RefWorks    
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.
Keywords Batch processing      Sanger sequences      Contig assembly      SeqMan     
Fund:The development of this package was supported by the National Natural Science Foundation of China (31671326) and the Youth Innovation Promotion Association, Chinese Academy of Sciences *Corresponding author, E-mail: sunyanbo@mail.kiz.ac.cn
Corresponding Authors: Yan-Bo Sun,E-mail: sunyanbo@mail.kiz.ac.cn    
Service
E-mail this article
E-mail Alert
RSS
Articles by authors
Cite this article:   
Jie-Qiong Jin, Yan-Bo Sun. AutoSeqMan: batch assembly of contigs for Sanger sequences. Zoological Research, 2018, 39(2): 123-126.
URL:  
http://www.zoores.ac.cn/EN/10.24272/j.issn.2095-8137.2018.027     OR     http://www.zoores.ac.cn/EN/Y2018/V39/I2/123
[1] Yan-Bo Sun. FasParser: a package for manipulating sequence data[J]. ZOOLOGICAL RESEARCH, 2017, 38(2): 110-112.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed