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 [email protected].

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