#### Chlamydia genome comparison
Here we provide supplemental information about our comparative genome analysis of 33 _Chlamydia_ strains that revealed characteristic features of avian host preference.
If you use this data please cite:
[Hölzer and Barf _et al._ "Comparative genome analysis of 33 _Chlamydia_ strains reveals characteristic features of _Chlamydia psittaci_ and closely related species", _MDPI Pathogens_, 2020](https://doi.org/10.3390/pathogens9110899)
In this repository you find:
* sequences of the 33 genomes used in this study
* including also the 8 newly sequenced and assembled genomes
* we also provide an additional file only containing the 8 new assemblies
* re-annotations for all genomes w/ [Prokka](https://github.com/tseemann/prokka)
* core gene calculations using [RIBAP](http://github.com/hoelzer-lab/ribap)
* for all 33 genomes
* for all 12 type strains
Raw sequencing data of the eight novel _de novo_ assemblies are hosted at [ENA PRJEB40883](https://www.ebi.ac.uk/ena/browser/view/PRJEB40883).
To reproduce our core gene calculations, download the genomes and run:
```bash
nextflow run hoelzer-lab/ribap -r v0.4 --fasta '*.fasta' --tmlim 240 --tree
```
The `--tmlim` parameter controls how long GLPK will try to solve each individual ILP.
The RIBAP HTML output table can be also explored [here](https://www.rna.uni-jena.de/supplements/chlamydia_genome_comparison/2020-06-05/web/ribap.html).
