Listeria plasmid data

<p>Data for analysis of Listeria plasmids</p> <p>&nbsp;</p> <p>Assemblies were downloaded from NCBI and analyzed with the MOB-suite. The MOB-recon results for all of the assemblies is available &ldquo;mob.recon.tar.gz&rdquo; and the original assemblies can be reconstructed by &ldquo;cat {acs}/*.fasta &gt; {acs}.fasta&rdquo;. 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 &ldquo;mob.results.tar.gz&rdquo;&nbsp; is split into 2GB files with the suffix {part[A-V]}. The tarball can be reconstructed by doing &ldquo;cat mob.recon.tar* &gt; mob.results.tar.gz&rdquo;.</p> <p>&nbsp;</p> <p>On the original assemblies, the samples were typed according to the 7-gene MLST scheme using mlst (<a href="https://github.com/tseemann/mlst">https://github.com/tseemann/mlst</a>) v2.23.0 and the lineage, and CC added based on the table provided by the Pasteur institute</p> <p>&nbsp;</p> <p>Using abricate v1.0.0 (<a href="https://github.com/tseemann/abricate">https://github.com/tseemann/abricate</a>) I have performed gene finding for BacMet db (<a href="https://github.com/jrober84/bacmet">https://github.com/jrober84/bacmet</a>) &ldquo;merged.bacmet.txt &ldquo;, VFDB &ldquo;merged.vfdb.txt&rdquo;.&nbsp;&nbsp;</p> <p>&nbsp;</p> <p>Chewbbaca cgMLST Allele calls for each genome and a profile of all of the allele calls is provided &quot;chew.alleles.profiles.txt.gz&quot;.&nbsp;</p> <p>&nbsp;</p> <p>Sample Metadata master table &ldquo;ListeriaSampleManifest.xlsx&rdquo;, there are samples which are not in pathogen&nbsp; detection and so do not have additional metadata associated with them. The metadata would need to be extracted from the SRA.&nbsp; This also needs to be standardized and cleaned up for analysis.</p>