MGCA

Microbial genome component and annotation pipeline

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  Introduction

The software under designing dedicates to perform the following analysis:

Genomic Component

HGT

• Genomic Island

• Prophage

• CRISPR-Cas

Repeat Sequences

• Tandem Repeats
• Interspersed Repeats

Non-coding RNA

• rRNA
• tRNA
• sRNA

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

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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

# Install mamba first
conda install mamba

# Usually specify the latest version of MGCA

mamba create -n mgca mgca=0.0.0

# 上面的命令提示找不到mgca的话，用下面这条来安装

mamba create -n mgca https://anaconda.org/bioconda/mgca/0.0.0/download/noarch/mgca-0.0.0-pl5321hdfd78af_0.tar.bz2

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

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emboss

islandpath

opfi

Perl & the modules

perl-bioperl

phispy 4.2.21

R & the packages

ggplot2

wget

In the future:

    #- gtdbtk
    #- bakta (include trnascan-se infernal piler-cr)
    #- repeatmasker (include trf)
    #- mummer4
    #- artemis (include openjdk)
    #- saspector (include trf progressivemauve prokka)
    #- lastz
    #- kakscalculator2
    #- interproscan (include emboss openjdk)
    #- eggnog-mapper (include wget)

Usage

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Print the help messages:

mgca --help

General usage:

mgca [modules] [options]

Modules:

[--PI] Calculate statistics of protein properties and print pI of all protein sequences

[--IS] Predict genomic island from GenBank files

[--PROPHAGE] Predict prophage sequences from GenBank files

[--CRISPR] Finding CRISPR-Cas systems in genomics or metagenomics datasets

Examples

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Example 1: Calculate statistics of protein properties and print pI of all protein sequences

mgca --PI --AAsPath <PATH> --aa_suffix <.faa>

Example 2: Predict genomic island from GenBank files

mgca --IS --gbkPath <PATH> --gbk_suffix <.gbk>

Example 3: Predict prophage sequences from GenBank files

mgca --PROPHAGE --gbkPath <PATH> --gbk_suffix <.gbk> --phmms <Path of pVOG.hmm> --phage_genes <1> --min_contig_size <5000> --threads <6>

Example 4: Finding CRISPR-Cas systems in genomics or metagenomics datasets

mgca --CRISPR --scafPath <PATH> --scaf_suffix <.fa> --casDBpath <db path> --threads <6>

OUTPUT

PI

Results/PI/*.pepstats: Peptide statistics for each protein sequence organized by the genome.

Results/PI/*.pI: Protein isoelectric point and its frequency.

Results/PI/*.pI.tiff: A plot drawing 'Relative frequency' vs. 'isoelectric point'.

IS

Results/IS/All_island.list: A list file containing genomic island information.

Results/IS/All_island.txt: A file contains information and sequence of genes in the genomic island.

PROPHAGE

Results/PROPHAGE/*_prophage: Result for each genome.

Results/PROPHAGE/All.prophages.txt: The summary results (for all genomes) include information of prophage on the host genome.

Results/PROPHAGE/All.prophages.seq: The summary results (for all genomes) include information of prophage genes and sequences.

CRISPR

Results/CRISPR/*_intially: Results obtained by permissive BLAST parameters (In most cases, it can be ignored).

Results/CRISPR/*_filtered: The results obtained after *_intially quality control (The final result).

Results/CRISPR/*_filtered/*.csv: The file contains information of CRISPR array.

Results/CRISPR/*_filtered/*.png: The visualizations of all predicted CRISPR array, as shown below:

License

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MGCA is free software, licensed under GPLv3.

Feedback and Issues

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

Citation

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

Updates

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V0.0.0

The MGCA was born.