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PanMAN Construction

Here, we will learn to build PanMAN from various input formats.

Step 0: The Steps below require panmanUtils, if not done so far, refer to installation guide to install panmanUtils. To check if panmanUtils is properly installed or not, run the following command, and it should execute without error 

# enter into the panman directory (assuming $PANMAN directs to the panman repository directory)
cd $PANMAN_HOME

cd $PANMAN_HOME/build
./panmanUtils --help

Building PanMAN from PanGraph

Step 1: Check if sars_20.json and sars_20.nwk files exist in test directory. Alternatively, users can provide custom PanGraph (JSON) and tree topology (Newick format) files to build a panman.

Step 2: Run panmanUtils with the following command to build a panman from PanGraph:

cd $PANMAN_HOME/build
./panmanUtils -P $PANMAN_HOME/test/sars_20.json -N $PANMAN_HOME/test/sars_20.nwk -O sars_20
The above command will run panmanUtils program and build sars_20.panman in $PANMAN_HOME/build/panman directory.

Building PanMAN from GFA

Step 1: Check if sars_20.gfa and sars_20.nwk files exist in test directory. Alternatively, users can provide custom GFA and tree topology (Newick format) files to build a panman.

Step 2: Run panmanUtils with the following command to build a panman from GFA:

cd $PANMAN_HOME/build
./panmanUtils -G $PANMAN_HOME/test/sars_20.gfa -N $PANMAN_HOME/test/sars_20.nwk -O sars_20
The above command will run panmanUtils program and build sars_20.panman in $PANMAN_HOME/build/panman directory.

Building PanMAN from MSA (FASTA format)

Step 1: Check if sars_20.msa and sars_20.nwk files exist in test directory. Alternatively, users can provide custom MSA (FASTA format) and tree topology (Newick format) files to build a panman.

Step 2: Run panmanUtils to build a panman from GFA using the following commands:

cd $PANMAN_HOME/build
./panmanUtils -M $PANMAN_HOME/test/sars_20.msa -N $PANMAN_HOME/test/sars_20.nwk -O sars_20
The above command will run panmanUtils program and build sars_20.panman in $PANMAN_HOME/build/panman directory.

Building PanMAN from raw genome sequences

We provide scripts to construct panmanUtils inputs (PanGraph/GFA/MSA and Newick) from raw sequences (FASTA format), followed by building a panman.

Note

This script uses various tools such as PanGraph tool, PGGB, MAFFT, and MashTree to build input PanGraph, GFA, MSA, and Tree topology files, respectively. The script is particularly designed to be used in the docker container build from either the provided docker image or the DockerFile (instructions provided here).

Step 1: Check if the sars_20.fa file exists in test directory. Alternatively, users can provide custom raw sequences (FASTA format) to build a panman.

Step 2: Run the following command to construct a panman from raw sequences.

cd $PANMAN_HOME/scripts
chmod +x build_panman.sh
./build_panman.sh pangraph/gfa/msa