Am looking at the schemes available via chewie-NS. Great initiative, but why have the genes been renamed? For instance, the Listeria one now has gene codes like "Pasteur_cgMLST-00089108.fasta", rather than the Pasteur LmoXXXX codes. Is there a conversion table? I noticed the same for the E. coli, Salmonella and Campylobacter ones.

Hi,

I only find the wgMLST schemas in the chewbie-NS server. Can you kindly let me know where I can find the cgMLST schemas for C.jejuni ? If not available, then kindly let us know the genomes used and I will try to find the cgMLST from it.

Best Regards,
Bala

Dear Chewie-NS team,

Is there any metadata (eg. Source, Year, etc..) related to historical data associated with the genomes used for the construction of external schema?

If so then kindly let us know so that we can able make use of it as in the innuendo project link below:

https://innuendo.readthedocs.io/en/latest/usage/set-legacy.html

I am attaching a reference metadata file for your reference where each row is a assembled genome of an isolate.

Yenterocolitica_metadata.txt

Kindly let us know the possibilities!

Best Regards,
Bala

Dear Chewie-NS server Team,

The size threshold parameter default (0.2) of chewbbaca is different from the schemas produced by Chewie-NS server (None) as shown below:

singularity exec -B $PWD:$PWD -B /mnt/THL_RV2/singularity_cache/:/mnt/THL_RV2/singularity_cache/ biocontainers-chewbbaca-2.5.6--py.img chewBBACA.py AlleleCall -i input_file.txt -g /mnt/THL_RV2/singularity_cache/shared_files/chewbbaca_test/campy -o chew_results --cpu 4 --ptf /mnt/THL_RV2/singularity_cache/shared_files/chewbbaca_test/campy/data/Campylobacter_jejuni.trn --st 0.2

chewBBACA version: 2.5.6
Authors: Mickael Silva, Pedro Cerqueira, Rafael Mamede
Github: https://github.com/B-UMMI/chewBBACA
Wiki: https://github.com/B-UMMI/chewBBACA/wiki
Tutorial: https://github.com/B-UMMI/chewBBACA_tutorial
Contacts: [email protected]

==========================
chewBBACA - AlleleCall

Provided arguments values differ from arguments values used for schema creation:

  Argument              Schema         Provided

size_threshold None 0.2

Continuing might lead to results not consistent with previous runs.
Providing parameters values that differ from the ones used for schema creation will also invalidate the schema for uploading and synchronization with the Chewie-NS.

So, We wonder any solutions from the chewbie-NS team to have the schemas produced at the same size threshold 0.2 by chewbbaca???

Any help on this is appreciated!

Best Regards,
Bala