Difference between revisions of "Build a core-genome phylogeny"
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=== Get table of genome assemblies === | === Get table of genome assemblies === | ||
| − | + | The list of available genome assemblies can be downloaded with the script <syntaxhighlight lang="Python" inline>get_genomes_chlassification.py</syntaxhighlight> | |
<syntaxhighlight lang="Bash" line='line'> | <syntaxhighlight lang="Bash" line='line'> | ||
df -h | df -h | ||
Revision as of 12:22, 24 October 2018
Overview
This tutorial describes step by step the reconstruction of a core genome phylogeny for a given clade of bacteria.
Setup
- clone eutils repository
1 # download repo from metagenlab 2 git clone https://github.com/metagenlab/eutils.git 3 # move to eutils directory 4 cd eutils 5 # add path to pythonpath and path 6 echo "export PATH=:$PWD"':$PATH' >> ~/.bashrc 7 echo "export PYTHONPATH=:$PWD"':$PYTHONPATH' >> ~/.bashrc 8 # reload bashrc 9 source ~/.bashrc
- install miniconda
- create a dedicated environment and install orthofinder
1# create a new environment 2conda create -n orthofinder 3source activate orthofinder 4# install orthofinder 5conda install orthofinder 6# install biopython 7conda install biopython
Get table of genome assemblies
The list of available genome assemblies can be downloaded with the script get_genomes_chlassification.py
1df -h
Download gbff files
1df -h