Listeria plasmid data

Data for analysis of Listeria plasmids

Assemblies were downloaded from NCBI and analyzed with the MOB-suite. The MOB-recon results for all of the assemblies is available “mob.recon.tar.gz” and the original assemblies can be reconstructed by “cat {acs}/*.fasta > {acs}.fasta”. It is roughly 45GB in size, so to save extra downloading issues it is provided as just the MOB-recon results. In order for the data to be uploaded to zenodo, the tarball had to be split into smaller-sized files. So “mob.results.tar.gz”  is split into 2GB files with the suffix {part[A-V]}. The tarball can be reconstructed by doing “cat mob.recon.tar* > mob.results.tar.gz”.

On the original assemblies, the samples were typed according to the 7-gene MLST scheme using mlst (https://github.com/tseemann/mlst) v2.23.0 and the lineage, and CC added based on the table provided by the Pasteur institute

Using abricate v1.0.0 (https://github.com/tseemann/abricate) I have performed gene finding for BacMet db (https://github.com/jrober84/bacmet) “merged.bacmet.txt “, VFDB “merged.vfdb.txt”.  

Chewbbaca cgMLST Allele calls for each genome and a profile of all of the allele calls is provided "chew.alleles.profiles.txt.gz". 

Sample Metadata master table “ListeriaSampleManifest.xlsx”, there are samples which are not in pathogen  detection and so do not have additional metadata associated with them. The metadata would need to be extracted from the SRA.  This also needs to be standardized and cleaned up for analysis.