PGCGAP - the Prokaryotic Genomics and Comparative Genomics Analysis Pipeline

Anyone who want a help from me, please create an Issue on GitHub. Sometimes, I can't send E-mail successfully to your mail server due to unknown reasons, sometimes. The user also can contact me by instant-messaging software，such as QQ (ID：518953730 or (ID: liaochenlanruo).

English Readme | Chinese Readme

      ____       ____      ____     ____       _        ____    
    U|  _"\ u U /"___|u U /"___| U /"___|u U  /"\  u  U|  _"\ u 
    \| |_) |/ \| |  _ / \| | u   \| |  _ /  \/ _ \/   \| |_) |/ 
     |  __/    | |_| |   | |/__   | |_| |   / ___ \    |  __/   
     |_|        \____|    \____|   \____|  /_/   \_\   |_|      
     ||>>_      _)(|_    _// \\    _)(|_    \\    >>   ||>>_    
    (__)__)    (__)__)  (__)(__)  (__)__)  (__)  (__) (__)__)   

Contents

• Introduction

• Installation

• Required dependencies

• License

• Feedback and Issues

• Citation

• Usages

Introduction

PGCGAP is a pipeline for prokaryotic comparative genomics analysis. It can take the pair-end reads as input. In addition to genome assembly, gene prediction and annotation, it can also get common comparative genomics analysis results such as phylogenetic trees of single-core proteins and core SNPs, pan-genome, whole-genome Average Nucleotide Identity (ANI), orthogroups and orthologs, COG annotations, substitutions (snps) and insertions/deletions (indels) and antimicrobial and virulence genes mining with only one line of commands.

Installation

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

Step1: Install PGCGAP

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

  # Install mamba first
  conda install mamba
  
  # Usually specify the latest version of PGCGAP
  mamba create -n pgcgap pgcgap=1.0.35

• Method 2: use \"environment.yaml\". Run the following commands to download the latest environmental file and install PGCGAP:

  # Install mamba first
  conda install mamba
  
  # download pgcgap.v1.0.35.yml
  wget --no-check-certificate https://bcam.hzau.edu.cn/PGCGAP/conda/pgcgap.v1.0.35.yml
  
  # create a conda environment named as pgcgap and install the latest version of PGCGAP
  mamba env create -f pgcgap.v1.0.35.yml -n pgcgap
  

Step2: Setup COG database (Users should execute this after first installation of pgcgap)

$conda activate pgcgap
$pgcgap --setup-COGdb
$conda deactivate

Users with docker container installed have another choice to install PGCGAP.

$docker pull quay.io/biocontainers/pgcgap:<tag>

(see pgcgap/tags for valid values for <tag>)

Required dependencies

• Abricate
• ABySS
• Canu
• CD-HIT
• Coreutils
• Diamond
• FastANI
• Fastme
• Fastp
• Htslib
• IQ-TREE
• Mafft
• Mash
• Mmseqs2
• Muscle
• NCBI-blast+
• OrthoFinder
• OpenJDK8
• PAL2NAL v14
• Panaroo
• Perl & the modules
  • perl-bioperl
  • perl-data-dumper
  • perl-file-tee
  • perl-getopt-long
  • perl-pod-usage
  • perl-parallel-forkmanager
• Prokka
• Python & the modules
  • biopython
  • matplotlib
  • numpy
  • pandas
  • seaborn
• R & the packages
  • corrplot
  • ggplot2
  • gplots
  • pheatmap
  • plotrix
• Sickle-trim
• Snippy
• Snp-sites
• trimAL
• unicycler
• wget

License

PGCGAP 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: Liu H, Xin B, Zheng J, Zhong H, Yu Y, Peng D, Sun M. Build a bioinformatics analysis platform and apply it to routine analysis of microbial genomics and comparative genomics. Protocol exchange, 2022. DOI: 10.21203/rs.2.21224/v6

Usages

For more detial informations, please visit the webpage of PGCGAP and WIKI.