Platform License GitHubversion Downloads conda install with bioconda BIOINFORMATICS

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 & Usage


See the official webpage for details.

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