Application of shell script in batch processing for Sanger sequencing results of enteroviruses

Abstract

Objective To create a shell script for the batch processing of Sanger sequencing results and sequence alignments of enteroviruses, e.g. coxsackievirus, and to prepared data files with standard format for further analysis. Methods The VP1 genes of enteroviruses, e.g. coxsackievirus were sequenced and the results were manually analyzed. A shell script was written to simulate manual analysis of the same sequence trace files. In the script, three softwares, phred, phd2fasta and phrap, and stand-alone NCBI-BLAST software were called in-turn to accomplish base-calling, file formatting, sequence assembly and alignment analysis. After alignment, a series of Linux text processing commands were used to generate files containing sample names, descriptions of reference sequences with the highest similarity, genotypes and files containing sequences for further analysis. To evaluate reliability of batch processing with the shell script, the similarity of sequences generated by the script and the sequences processed manually was analyzed by MEGA 6.0 software. Results The shell script accomplished all functions. The analysis results by the shell script were identical to those by manual analysis. Conclusions Applying shell script saved time and resources in sequencing results analysis. Researcher will be able to concentrate more on further analysis. Key words: Shell script; Sanger sequencing; Hand, foot, and mouth disease; Enterovirus