Downloading schemes

Before MiST can perform allele calling, you need a scheme containing reference alleles and (optionally) sequence type (ST) profiles. MiST provides helper scripts to download schemes from common sources.

⚠️ Important: After downloading, schemes must still be indexed before they can be used.

📌 Disclaimer: Make sure to cite the corresponding resources when using these schemes in your research.

Basic usage

The general command to download a scheme is:

mist download --downloader {SOURCE} --url {URL} --output scheme_out

Options

Options:
  --url TEXT                      URL to download from.  [required]
  -o, --output PATH               Output directory  [default: mist_download]
  -p, --include-profiles          Download the profiles
  -d, --downloader [cgmlstorg|enterobase|bigsdb|bigsdb_auth]
                                  Downloader  [required]
  --dir-tokens PATH               Directory with access tokens  [default:
                                  /scratch/temp/bebog/.bigsdb_tokens]
  --key-name TEXT                 Key name  [default: PubMLST]
  --site TEXT                     Site  [default: PubMLST]
  --debug                         Enable debug mode
  --log PATH                      Save log to this file
  --help                          Show this message and exit.

The currently supported values for the site option are PubMLST and Pasteur. The --key-name should correspond to the value in the access_tokens file in the token directory.

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EnteroBase

EnteroBase is a web platform for analyzing bacterial genomic data. MiST downloads schemes directly from the EnteroBase FTP site.

• Available schemes: EnteroBase schemes

Example command

mist download \
  --downloader enterobase \
  --url https://enterobase.warwick.ac.uk/schemes/Escherichia.Achtman7GeneMLST/ \
  --output enterobase_ecoli_mlst_achtman \
  --include-profiles 

How to cite

https://enterobase.warwick.ac.uk/cite

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BIGSdb (PubMLST, IP Paris) - without authentication

BIGSdb is software for storing and analyzing sequence data for bacterial isolates. It powers PubMLST.org and Institut Pasteur BIGSdb.

⚠️ Both PubMLST.org and BIGSdb IPP require authorization to access the most recently submitted data. See with-authorization.

Downloading a scheme

Determining the scheme URL

The URL of a scheme can be determined by searching for it on this page (sequence databases have the _seqdef suffix).

• https://rest.pubmlst.org/
• https://bigsdb.pasteur.fr/api

For example:

https://rest.pubmlst.org/db/pubmlst_abaumannii_seqdef

From this page, you can navigate to the available schemes by following the /schemes endpoint.

https://rest.pubmlst.org/db/pubmlst_abaumannii_seqdef/schemes

Example command

mist download \
  --downloader bigsdb \
  --url https://rest.pubmlst.org/db/pubmlst_abaumannii_seqdef/schemes/1 \
  --output pubmlst_abaumannii_mlst \
  --include-profiles 

How to cite

• PubMLST.org: https://pubmed.ncbi.nlm.nih.gov/30345391/.
• BIGSdb Institut Pasteur: See References section for each species on BIGSdb IP Paris.

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BIGSdb (PubMLST, IP Paris) - with authentication

BIGSdb instances require authentication to access the most recent data. MiST relies on the BIGSdb_downloader (bundled in MiST).

1. Setting up credentials

• Follow the credential setup guide
• Register for database access via My Account > Database registrations.
• Ensure the following files exist in your .bigsdb_tokens directory:

access_tokens
client_credentials

2. Example command

mist download \
  --downloader bigsdb_auth \
  --url https://rest.pubmlst.org/db/pubmlst_abaumannii_seqdef/schemes/1 \ 
  --token_dir /path/to/.bigsdb_tokens \
  --key-name PubMLST \
  --site PubMLST

Troubleshooting

• subprocess.TimeoutExpired: You likely do not have access. Register with the database first.
• Compare allele counts with and without authentication to confirm access.

How to cite

• PubMLST.org: https://pubmed.ncbi.nlm.nih.gov/30345391/.
• BIGSdb Institut Pasteur: See References section for each species on BIGSdb IP Paris.

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cgMLST.org

cgMLST.org provides curated cgMLST schemes.

The available schemes and corresponding URLs can be found here.

Example command

mist download \
  --downloader cgmlstorg \
  --url https://www.cgmlst.org/ncs/schema/Banthracis5268/ \
  --output cgmlstorg_banthracis \
  --include-profiles

How to cite

Each scheme lists its citation on cgMLST.org under the “citation” box.

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Next step Indexing schemes.