johnlees
commented
1 year ago Thanks for this contribution, we would be very happy to make this the updated version on the website as it sounds like you've done a much more thorough QC of the data. I might suggest that we use your sketches with the existing model fit, to maintain as much backwards compatibility as possible.
It may be convenient to upload your data here: https://imperialcollegelondon.app.box.com/f/3c4781a2f5ad4215b12a62099ed5cc63 Then I can run through with the previous model and update the website.
Please also let me know if you have any preferred citation or attribtion for this that you'd like me to include on the page.
tanzhizhou
Hi johnlees,
Please specify:
Is this a request for us to make a new database? No
Is this a database you have fitted, and wish us to add? Yes
If the latter:
What is the species? Neisseria meningitidis
How many genomes are included? 26801
Are the genomes public? Yes, All genomes were downloaded from PubMLST website.
Are the genomes published? Yes
How did you obtain your fit? the database was fitted to the dbscan model
I know that there is a database of Neisseria meningitidis already in your website, however, I found that the genome quality of Neisseria meningitidis in PubMLST is not good enough, and some isolates were even not belong to the species of Neisseria meningitidis.
For that reason, in this version of database, all the genomes of isolates were validated by species identification function (taxonomy_wf) in Genome Database Taxonomy toolkit (GTDB-Tk). Quality of the genomes were assessed using CheckM software. Of the isolates, only those with a completeness rate of ≥90% and a contamination rate of ≤5% were considered suitable for Poppunk model fitting and clustering.
Could I submit this database to your website?
Zhizhou Tan
Chinese CDC