MGCA

Microbial genome component and annotation pipeline

Introduction

The software under designing dedicates to perform the following analysis:

• Genomic Component
  • HGT
    • Genomic Island
    • Prophage
    • CRISPR-Cas
  • Non-coding RNA
    • rRNA
    • tRNA
    • sRNA
  • Repeat Sequences
    • Tandem Repeats
    • Interspersed Repeats
• Genomic Attributes
  • Genome Survey
  • Protein Properties
  • WGS-based Species Identify
• Function Annotation
  • General Annotation
    • SwissProt
    • Pfam
    • GO
    • KEGG
  • Target Gene Mining
    • Effectors
      • T3SS
      • T4SS
      • Secretory/Membrane/Intracellular Protein
      • Secondary Metabolite Biosynthetic Gene Clusters
    • Virulence/Pathogenicity/Resistance Gene
      • Antibiotic Resistance Genes (ARGs)
      • Pathogen Host Interactions (PHI)
      • Comprehensive Antibiotic Resistance Database (CARD)
    • Element Cycle
      • CAZyme
      • Nitrogen
      • Sulfur
      • Methane
    • Membrane Transport Protein (TCDB)
• Comparative Genomics
  • Collinearity
  • Positive Selection
  • SNP

NOTICE: It will take a long time to complete the development!

Installation

The software was tested successfully on Windows WSL, Linux x64 platform, and macOS. Because this software relies on a large number of other software, so it is recommended to install with Bioconda.

Step1: Install MGCA

• Method 1: use mamba to install MGCA ( is now avaliable)

    # Install mamba first
    conda install mamba
  	
    # Usually specify the latest version of PGCGAP
    mamba create -n mgca mgca=0.0.0
  

Step2: Setup database (Users should execute this after the first installation of mgca)

conda activate mgca
setupDB --all
conda deactivate

Notice: there is a little bug, users can edit the "setupDB" file located at the mgca installation path to resolve the problem. Just remove the lines after line no. 83.

Required dependencies

• artemis
• bakta
• eggnog-mapper
• emboss
• gtdbtk
• interproscan (include emboss openjdk)
• islandpath
• kakscalculator2
• lastz
• mummer4
• opfi
• Perl & the modules
  • perl-bioperl
• phispy
• R & the packages
  • ggplot2
• repeatmasker
• saspector (include trf progressivemauve prokka)

License

MGCA is free software, licensed under GPLv3.

Feedback and Issues

Please report any issues to the issues page or email us at liaochenlanruo@webmail.hzau.edu.cn.

Citation

If you use this software please cite: Hualin Liu. MGCA: microbial genome component and annotation pipeline. Avaliable at GitHub https://github.com/liaochenlanruo/mgca