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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
    

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Metagen-o-matic: Pipeline for metagenome analysis

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