PanACEA is a suite of PERL scripts that allows users to create an interconnected set of html, javascript and json files that allows for visualization of prokaryotic pan-chromosomes, including core and variable regions. Users can also include additional information such as gene annotation, metadata annotation, and genome phylogenies. Detailed information about the PanACEA suite and usages can be found in the PDF manual included on the site.
Also included in the Github is a set of exemplar data from a PanOCT run on 19 Acinetobacter baumannii complete genomes and a shell script which can generate the PanACEA output files from the examples is available as a demonstration.
Additionally, the gzipped output from a PanACEA run using the same data and the gzipped PanACEA output from the finished PanOCT run on Enterobactor hormaechei from Chavda et al 2016 are available.
The example data is the raw output from a PanOCT run on 19 A. baumannii genomes plus annotation that will allow the user to observe all the necessary steps to move from the raw files to the html files. Unix shell users such as Mac and Linux users can use the "./run_panacea_example.sh" in the git download directory to run all the steps. Likewise, Windows users can use the batch file in the same directory called "run_panacea_example.bat" to generate the PanACEA files. Finally, I have included a list of all four commands with $DIR as the git root directory:
- Makes the PanACEA flatfile
- perl $DIR\make_panacea_flatfile.pl -i $DIR\example_dir\ -o $DIR\example_dir\PanACEA.flatfile.txt -t Pangenome
- Makes the ARO list files from the RGI dataSummary table
- perl $DIR\make_rgi_clusters.pl -i $DIR\example_dir\dataSummary.txt -o $DIR\example_dir/aro_centroid.list.txt
- Makes the configure file for the annotation files
- perl $DIR\make_conf_file.pl -d $DIR\example_dir\ -o $DIR\example_dir\ -a $DIR\aro.obo -g $DIR\gene_ontology.1_2.obo
- Makes all the output HTML, JSON and javscript files
- perl $DIR\make_panacea.pl -i $DIR\example_dir\PanACEA.flatfile.txt -o $DIR\example_dir\ -f $DIR\example_dir\func_file.conf.txt -t $DIR\example_dir\genomes.tree -a $DIR\example_dir\cluster_alignments,$DIR\example_dir\combined.fasta
make_panacea.pl generates an interconnected set of html, javascript and json files from a PanACEA flat file generated from a possible suite of programs, including PanOCT, that allows users to explore multiple related prokaryotic genomes through their pan-chromosomes, including core and flexible regions. While the basic version only shows the location and relative position of the core and flexible regions, the user can also add information on the gene cluster annotation and alignment as well as the genomic annotation and phylogeny to obtain a more complete view of the relationship between the genomes, their function and any regions with their associated genes that might drive this relationship. The end result is a central html file that can be opened in many web browsers.
running make_panacea.pl
make_panacea.pl [options]
Options:
-i --input Input PanACEA Flat File. Required.
-o --output Output Directory for all the files. Default is current directory.
-n --name Header name of HTML and SVG files. Default is \"PanHTML\"
-d --dir_name Root directory of the HTML for use in the browser. Default is current directory.
-f --function File containing information about additional gene cluster annotation.
-a --fasta Either directory containing the cluster multiple alignment files or a single fasta file. Multiple inputs could be added in a comma separated list
-t --tree File containing the phylogeny of the genomes in newick format. (Requires BioPerl to use)
-m --metafiles File containing group metadata for the genomes. Only used in connection with tree.
-g --graphic File containing the graphics configure file to change the size of the whole image and parts of the image
make_panacea_flatfile.pl generates the panchromosome PanACEA flat file from pangenome output from various programs, including PanOCT. This file is required to run the PanACEA visualizer.
running make_panacea_flatfile.pl
make_panacea_flatfile.pl [options]
Options:
-i --input Input directory of the Pangenome information. Required.
-o --output Output file. Default is PanACEA.[date].txt
-t --type Input type of the Pangenome. Currently supports "Pangenome" <default>, Pangenome "Iterative", and "Panoct".
make_conf_file.pl generates a functional configuration file used by make_panacea.pl to color the genes and make the tables for the terms. It is designed to work on the output of the JCVI Pangenome pipeline.
running make_conf_file.pl
make_conf_file.pl [options]
Options:
-d --dir input pangenome directory. Default is current directory
-o --out output directory. Default is current directory
-g --go location of go term obo file. Default is current directory
-a --aro location of aro obo file. Default is current directory
-h --help
make_rg\i_clusters.pl translates the RGI output file dataSummary.txt into the PanGenome annotation table format. Required to make it readable for PanACEA. Either best or all hits can be outputed
running make_rgi_clusters.pl
make_rgi_clusters.pl [options] -d directory -t type -o outputFlatFile
Options:
-i --input Location of the dataSummary.txt file. Required
-o --output output file. Default is "aro_centroid.list.txt" in the current directory
-t --type Output type of the file, either "best" (only the best hit) or "all". Best is default
PDF manual including screen shots and usage guides for both the command line and the web interface for PanACEA
Shell script to run the scripts required to build the PanACEA web pages for the example data
Directory containing the example PanACEA data derived from the PanOCT run on the 19 Acinetobacter genomes:
Compressed file containing the multi-file output of the PanACEA run on Enterobactor cited in Chan et al 2016.
Compressed file containing the multi-file output of the PanACEA run on Acinetobacter genomes in the example files