efaecium-niche

Code for reproducing e. faecium niche paper results.

0. Compute tools

External tools are available for the download and processing of our data.

Data downloader

Download Dr. Finlay Maguire's data aqcusition tool from here.
git clone https://github.com/fmaguire/enterococcus_sample_reconciliation

ARETE pipeline

A bulk of the data processing and analysis in this work can be replicated by running the ARETE Nextflow pipeline, a pipeline designed for end-to-end assembly and annotation of bacterial genomes.
Download the code from here: git clone https://github.com/beiko-lab/arete

BayesTraits

You will need to install the BayesTraits executable from (here)[http://www.evolution.rdg.ac.uk/].

IslandCompare

TODO

DBSCAN-SWA

TODO

1. Download the data and metadata

bash enterococcus_sample_reconciliation/genomes/download.sh
todo: upload script that extracts faecium only, make into ARETE sample sheet
todo: reference and outgroup genomes

2. Run ARETE

Requires Nextflow, Singularity.

nextflow run arete/ --input_sample_table data/samplesheet.py --reference_genome data/Efaecium_DO.fasts --outgroup_genome data/ehirae.fasta -entry assembly -profile singularity
mv results assembly
python filter_assemblies.py
nextflow run arete/ --input_sample_table data/assemmblysheet.py --reference_genome data/Efaecium_DO.fasts --outgroup_genome data/ehirae.fasta -entry annotation -profile singularity

3. Run data post-processing scripts

1. filter_sort_concat.py
2. crosstab
3. BayesTraits

4. Run IslandCompare and DBSCAN-SWA

TODO

5. Create figures and tables

Simply open the Figures.ipynb and Tables.ipynb and run them.