Build a core-genome phylogeny

Overview

This tutorial describes step by step the reconstruction of a core genome phylogeny for a given clade of bacteria.

Setup

1. 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
   

2. install miniconda
3. 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_ncbi_genome_assemblies.py. Various options are available to filter the data in various ways:

• include only complete genomes
• include only representative or reference genomes (as classified on the NCBI)
• exclude incompletely classified genomes
• exclude genomes derived from metagenomes

If your taxon of interest includes too many genomes, it is also possible to get only one representative genome per species (or per genus/family/order). If you do so, one genome is selected among all assemblies available for each species. The genome is not selected randomly: priority is given to 1) complete genomes 2) reference genomes 3) representative genomes.

usage: get_ncbi_genome_assemblies.py [-h] [-t TAXON_ID] [-c] [-rf] [-rp] [-rs]
                                     [-gb] [-md] [-e] [-d] [-ra RANK]
                                     [-o OUTPUT]

optional arguments:
  -h, --help            show this help message and exit
  -t TAXON_ID, --taxon_id TAXON_ID
                        taxon_idd
  -c, --complete        Filter complete genomes (default: False)
  -rf, --reference      Filter reference genomes (default: False)
  -rp, --representative
                        Filter representative genomes (default: False)
  -rs, --refseq         Filter refseq assemblies (default: False)
  -gb, --genbank        Filter genbank assemblies (default: False)
  -md, --exclude_metagenome_derived
                        Exclude metagenome derived assemblies (default: False)
  -e, --exclude_unclassified
                        Exclude species labelled as "unclassified xxx" or as
                        "xxxx sp. yyy" (e.g. Blautia sp. TF11-31AT)
                        (default=False)
  -d, --complete_list   Report complete list of assemblies (no taxonomy
                        clustering) (default: False)
  -ra RANK, --rank RANK
                        Keep one prepresentative/clade of specified taxonomic
                        <rank>
  -o OUTPUT, --output OUTPUT
                        Output name (default: assemblies_<taxid>.tab )

Example: get one assembly per species for the Lachnospiraceae family

1. go on the NCBI taxonomy website and search

[File:NCBI_taxid.png]

Download gbff files

1df -h