Listing schemes

The mist list command allows you to retrieve a list of schemes that can be downloaded. Each entry includes the scheme name and a corresponding URL. You can then pass this URL to the mist download script to download the scheme.

Examples

EnteroBase

To list available schemes from EnteroBase:

mist list --downloader enterobase

Example output (scheme name followed by URL):

Escherichia.Achtman7GeneMLST    https://enterobase.warwick.ac.uk/schemes/Escherichia.Achtman7GeneMLST/
Escherichia.cgMLSTv1            https://enterobase.warwick.ac.uk/schemes/Escherichia.cgMLSTv1/
...
Salmonella.wgMLST               https://enterobase.warwick.ac.uk/schemes/Salmonella.wgMLST/

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cgMLST.org

To list available schemes from cgMLST.org:

mist list --downloader cgmlstorg

Example output:

Acinetobacter baumanniicgMLST   https://www.cgmlst.org/ncs/schema/Abaumannii6032/
Bacillus anthraciscgMLST        https://www.cgmlst.org/ncs/schema/Banthracis6047/
...
Yersinia enterocoliticacgMLST   https://www.cgmlst.org/ncs/schema/Yenterocolitica6022/

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BIGSdb

BIGSdb hosts many schemes, organized into sub-databases (usually by species). Retrieving schemes from BIGSdb is a two-step process:

1. List available sub-databases

mist list --downloader bigsdb --host pubmlst

Example output:

Achromobacter spp.             pubmlst_achromobacter_seqdef
Acinetobacter spp.             pubmlst_abaumannii_seqdef
...
Yersinia spp.                  pubmlst_ypseudotuberculosis_achtman_seqdef

2. List schemes for a sub-database

Use the --db option to specify the sub-database name returned in the previous step.

mist list --downloader bigsdb --host pubmlst --db pubmlst_abaumannii_seqdef

Example output:

MLST (Oxford)                  https://rest.pubmlst.org/db/pubmlst_abaumannii_seqdef/schemes/1
MLST (Pasteur)                 https://rest.pubmlst.org/db/pubmlst_abaumannii_seqdef/schemes/2
...
Quorum sensing                 https://rest.pubmlst.org/db/pubmlst_abaumannii_seqdef/schemes/7

Notes

• The --host option must be specified (pubmlst or pasteur).
• Both bigsdb and bigsdb_auth downloaders retrieve scheme metadata without requiring authentication.

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Next step: Downloading schemes.