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Zoological Research
Kunming Institute of Zoology, Chinese Academy of Sciences
ISSN: 2095-8137
Vol. 39, No. 2, 2018, pp. 123-126
Bioline Code: zr18014
Full paper language: English
Document type: Report
Document available free of charge

Zoological Research, Vol. 39, No. 2, 2018, pp. 123-126

 en AutoSeqMan: batch assembly of contigs for Sanger sequences
Jin, Jie-Qiong & Sun, Yan-Bo

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

 
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