# pgcgap **Repository Path**: liaochenlanruo/pgcgap ## Basic Information - **Project Name**: pgcgap - **Description**: The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline - **Primary Language**: Perl - **License**: GPL-3.0 - **Default Branch**: master - **Homepage**: https://liaochenlanruo.fun/pgcgap/ - **GVP Project**: No ## Statistics - **Stars**: 0 - **Forks**: 0 - **Created**: 2022-02-18 - **Last Updated**: 2025-04-15 ## Categories & Tags **Categories**: Uncategorized **Tags**: None ## README # PGCGAP - the Prokaryotic Genomics and Comparative Genomics Analysis Pipeline ![](https://img.shields.io/badge/Platform-WSL%2FLinux%2FmacOS-green) [![GitHub license](https://img.shields.io/github/license/liaochenlanruo/pgcgap)](https://github.com/liaochenlanruo/pgcgap/blob/master/LICENSE) [![Version](https://anaconda.org/bioconda/pgcgap/badges/version.svg)](https://anaconda.org/bioconda/pgcgap) ![Downloads conda](https://img.shields.io/conda/dn/bioconda/pgcgap.svg?style=flat) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pgcgap/README.html)

**Anyone who want a help from me, please create an [Issue](https://github.com/liaochenlanruo/pgcgap/issues) 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](https://jq.qq.com/?_wv=1027&k=b59RfLly) or ![WeChat](https://badges.aleen42.com/src/wechat.svg) (ID: liaochenlanruo).** [English Readme](https://liaochenlanruo.github.io/pgcgap?_blank) | [Chinese Readme](https://liaochenlanruo.github.io/2019/04/28/PGCGAP%E4%B8%AD%E6%96%87%E8%AF%B4%E6%98%8E/?_blank) ____ ____ ____ ____ _ ____ U| _"\ u U /"___|u U /"___| U /"___|u U /"\ u U| _"\ u \| |_) |/ \| | _ / \| | u \| | _ / \/ _ \/ \| |_) |/ | __/ | |_| | | |/__ | |_| | / ___ \ | __/ |_| \____| \____| \____| /_/ \_\ |_| ||>>_ _)(|_ _// \\ _)(|_ \\ >> ||>>_ (__)__) (__)__) (__)(__) (__)__) (__) (__) (__)__) ## Contents - [Introduction](#introduction) - [Installation](#installation) - [Required dependencies](#required-dependencies) - [License](#license) - [Feedback and Issues](#feedback-and-issues) - [Citation](#citation) - [Usages](#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](https://bioconda.github.io/index.html)__. __Step1: Install PGCGAP__ - Method 1: use mamba to install PGCGAP ([![GitHubversion](https://anaconda.org/bioconda/pgcgap/badges/version.svg)](https://anaconda.org/bioconda/pgcgap) is now avaliable) ```bash # 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](https://bcam.hzau.edu.cn/PGCGAP/conda/pgcgap.v1.0.34.yml) and install PGCGAP: ```bash # 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](https://hub.docker.com/) installed have another choice to install PGCGAP. ``` $docker pull quay.io/biocontainers/pgcgap: ``` (see [pgcgap/tags](https://quay.io/repository/biocontainers/pgcgap?tab=tags) for valid values for <tag>) ## Required dependencies - [Abricate](https://github.com/tseemann/abricate) - [ABySS](http://www.bcgsc.ca/platform/bioinfo/software/abyss/) - [Canu](http://canu.readthedocs.org/) - [CD-HIT](http://weizhongli-lab.org/cd-hit/) - [Coreutils](https://www.gnu.org/software/coreutils/) - [Diamond](https://github.com/bbuchfink/diamond) - [FastANI](https://github.com/ParBLiSS/FastANI) - [Fastme](http://www.atgc-montpellier.fr/fastme/binaries.php) - [Fastp](https://github.com/OpenGene/fastp) - [Htslib](https://github.com/samtools/htslib) - [IQ-TREE](http://www.iqtree.org/) - [Mafft](https://mafft.cbrc.jp/alignment/software/) - [Mash](https://github.com/marbl/Mash) - [Mmseqs2](https://github.com/soedinglab/mmseqs2) - [Muscle](https://www.ebi.ac.uk/Tools/msa/muscle/) - [NCBI-blast+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) - [OrthoFinder](https://github.com/davidemms/OrthoFinder) - [OpenJDK8](https://openjdk.java.net/) - [PAL2NAL v14](http://www.bork.embl.de/pal2nal/) - [Panaroo](https://github.com/gtonkinhill/panaroo) - [Perl](http://www.perl.org/get.html) & the modules - [perl-bioperl](http://metacpan.org/pod/BioPerl) - [perl-data-dumper](http://metacpan.org/pod/Data::Dumper) - [perl-file-tee](http://metacpan.org/pod/File::Tee) - [perl-getopt-long](http://metacpan.org/pod/Getopt::Long) - [perl-pod-usage](http://search.cpan.org/~marekr/Pod-Usage-1.69/) - [perl-parallel-forkmanager](https://metacpan.org/pod/release/DLUX/Parallel-ForkManager-0.7.5/ForkManager.pm) - [Prokka](https://github.com/tseemann/prokka) - [Python](https://www.python.org/) & the modules - [biopython](https://biopython.org/) - [matplotlib](https://matplotlib.org/) - [numpy](http://www.numpy.org/) - [pandas](http://pandas.pydata.org/) - [seaborn](http://seaborn.pydata.org/) - [R](https://www.r-project.org/) & the packages - [corrplot](https://cran.r-project.org/web/packages/corrplot/index.html) - [ggplot2](https://cran.r-project.org/web/packages/ggplot2/) - [gplots](https://cran.r-project.org/web/packages/gplots/) - [pheatmap](https://cran.r-project.org/web/packages/pheatmap/index.html) - [plotrix](https://cran.r-project.org/web/packages/plotrix/) - [Sickle-trim](https://github.com/najoshi/sickle) - [Snippy](https://github.com/tseemann/snippy) - [Snp-sites](https://github.com/sanger-pathogens/snp-sites) - [trimAL](http://trimal.cgenomics.org/) - [unicycler](https://github.com/rrwick/Unicycler) - [wget](https://www.gnu.org/software/wget/) ## License PGCGAP is free software, licensed under GPLv3. ## Feedback and Issues Please report any issues to the [issues page](https://github.com/liaochenlanruo/pcgap/issues) or email us at [liaochenlanruo@webmail.hzau.edu.cn](mailto: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](https://doi.org/10.21203/rs.2.21224/v6) ## Usages For more detial informations, please visit the webpage of [PGCGAP](https://liaochenlanruo.github.io/pgcgap?_blank) and [WIKI](https://github.com/liaochenlanruo/pgcgap/wiki).