## Content
Here we list which intermediate and result files can be found in this repository accompanying our comparative genome study of _C. psittaci_ strains.
### Genome sequences
* n=63 genomes downloaded initially from NCBI (no further filters or decontamination applied, but n=7 duplicates removed)
* of these, n=50 genomes were finally selected after decontamination via [CLEAN](https://github.com/hoelzer/clean) and assembly qc filtering
* n=38 of the 63 NCBI genomes were re-assembled via available raw read sequencing data
* of those, n=11 were selected to replace NCBI assemblies due to better assembly and annotation quality and also after decontamination and qc
* after assembly qc, n=61 genomes (n=11 re-assembled, n=50 from NCBI; both after additional decontamination) were finally used in the comparative study
### Pan-genome via RIBAP
* a pan-genome and core gene set was calculated for all n=61 finally selected genomes via [RIBAP](https://github.com/hoelzer-lab/ribap) and the results added to this repository
### QUAST
* QUAST results for the 38 re-assembled strains and corresponding NCBI genomes
### IDEEL
* [IDEEL](http://www.opiniomics.org/a-simple-test-for-uncorrected-insertions-and-deletions-indels-in-bacterial-genomes/) plots comparing the 38 re-assembled and corresponding NCBI genomes regarding CDS fragmentation
### Plasmids
We extracted sequences of 47/61 plasmids from the final collection of strains included in our study for further assessment. The set of 47 plasmids is derived from:
* n=25 plasmids from NCBI assemblies
* n=19 plasmids from re-assemblies of raw read data for strains w/o any NCBI plasmid available
* n=3 plasmids from re-assemblies of raw read data for strains with low quality NCBI plasmids, namely: MN, Ho_Re_lower, Ho_Re_upper - so actually n=28 found in NCBI but only 25 used)
__If you use these data please cite:__ [Sachse, K., Hölzer, M., Vorimore, F., Barf, L.M., Lamkiewicz, K., Sachse, C., Laroucau, K. and Marz, M., 2022. Extensive genomic divergence among 61 strains of Chlamydia psittaci. _bioRxiv_.](https://www.biorxiv.org/content/10.1101/2022.11.10.515926v1.abstract)
