Metagen-o-matic

Pipeline for automated analysis of metagenomic data

Whole Metagenome Sequencing (WMS) data

1. ./pipe_wgs_preproc.sh

   • Description: Pre-processing of reads (adapter and quality trimming)
   • Parameters:
     • Input directory
     • An identifier for the analysis
     • Output directory
   • Example:

   ./pipe_wgs_preproc.sh ./indir example ./procdir > ./pipe_wgs_preproc.out.txt 2> ./pipe_wgs_preproc.err.txt
   

2. pipe_wgs_asm_pe.sh

   • Description: Assemble reference metagenome sequences based on sequencing reads data.
   • Parameters:
     • Input directory
     • Regular expression used to capture sample name patterns and group samples from biological replicates of the same sample groups
     • An identifier for the analysis
   • Example:

   ./pipe_wgs_asm_pe.sh ./procdir/example '^(sample.)' example > ./pipe_wgs_asm_pe.out.txt 2> ./pipe_wgs_asm_pe.err.txt
   

3. pipe_wgs_map.sh

   • Description: Taxonomic and functional annotation
   • Parameters:
     • Input directory
     • An identifier for the analysis
   • Example:

   ./pipe_wgs_map.sh ./procdir/example example > ./pipe_wgs_map.out.txt 2> ./pipe_wgs_map.err.txt