Classifying the Genomes of E. coli Strains

This analysis is part of a forthcoming manuscript entitled Classifying Bacterial Genomes Below the Species Rank.

Authors

Beatriz Vieira Mourato, Sara-Lena Welk, Fabian Klötzl, and Bernhard Haubold

Dependencies

This tutorial has six main dependencies:

• Neighbors for finding target and neighbor genomes
• datasets and dataformat for downloading and analyzing genomes
• Fur for finding unique genome regions
• Prim for designing PCR primers
• Biobox for general sequence manipulation
• the Unix tools curl, bzip2, and zip for downloading and decompressing files

If you are on a Debian system like WSL/Ubuntu, you can install these dependencies into ~/bin/ by executing from inside the o111h8 repo

bash scripts/setup.sh

Once that’s done, make sure ~/bin/ is in your path by running

source ~/.profile

We have tested this setup on our “minimal box” Docker container, mix.

Download and Construct Data Set

Execute

make data

to generate the directory data and download the Neighbors database, neidb, inside it. Since neidb is 1.3 GB large, this takes a couple of minutes, depending on the speed of your internet connection. The result consists of four files inside data,

• neidb, the Neighbors database calculated from the Genbank assemblies, Refseq assemblies, and the taxonomy database downloaded from the NCBI on 17th June 2026
• eco.json, the genome summaries of the 7884 E. coli genomes assembled to level “complete”
• eco.nwk, the tree of the 7361 complete E. coli genomes that passed the quality filter
• sero.txt, the serotypes of the 7361 complete E. coli genomes calculated with ectyper
• mlst.txt, the sequence types of the 7361 complete E. coli genomes retrieved using the program mlst

Tutorial

Make the tutorial and change into it.

make tutorial

This now contains the scripts and data files for following the tutorial described in the doc. We can also run all scripts to test them.

cd tutorial
bash testTut.sh