License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: August 03, 2022
Last Modified: August 05, 2022
Protocol Integer ID: 68154
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Abstract
This is a protocol for using PhaME to generate a phylogenomic tree from a set of Xanthomonas spp. genome sequences.
Create a directory for downloaded genome sequence data:
Command
Create directory (Ubuntu 22.04)
mkdir genomes
Enter the directory for downloaded genome sequence data:
Command
Enter directory (Ubuntu 22.04)
cd genomes
Ensure that NCBI Datasets command line tools are installed and executable (or a symbolic link to the executable) is in the current directory.
Software
NCBI Datasets command line tools
NAME
NCBI
DEVELOPER
Download the genome assemblies that will be included in the analysis:
Change back to the root directory (Ubuntu 22.04 LTS)
cd -
Set-up the working directory.
Command
Create working directory (Ubuntu 20.04 LTS)
mkdir workdir
Command
cd workdir
Command
Make symbolic links to all the genome assemblies (Ubuntu 22.04 LTS)
ln -s ../genomes/*.contig .
Optionally, at this point, we can delete the symbolic links for any genomes that we want to exclude from the final analysis. It is also an option to add any genome assemblies as .contig files (inf FASTA format).
Command
Return to previous directory (Ubuntu 22.04 LTS)
cd -
Install PhaME software into a Conda environment called 'phame', following instructions on the software's GitHub page:
Shakya M, Ahmed SA, Davenport KW, Flynn MC, Lo CC, Chain PSG (2020). Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life.. Scientific reports.
Shakya M, Ahmed SA, Davenport KW, Flynn MC, Lo CC, Chain PSG. Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life.