GutBlastocystis

Function

This pipeline is working for identification of Blastocystis sp. subtype 3 in metagenomic samples. The script is writen by Perl.

Author

Wen Zhang, zhangwen@icdc.cn

Dependent Software

Bowite2 samtools bcftools Perl

Usage

perl Blastocystis_finder.pl -fq1 or perl Blastocystis_finder.pl -fq1 -fq2

Input

fastq format file (SE file or PE files)

Output

(1) sam align files (2) snp list to ref seq (3) Report files (Covereage,Depth)