Please provide information on the sequencing and assembly technologies used in the submission messages section

📋 Data requirements

Users are requested to submit only high-quality assemblies, generated from pure cultures and sequenced at a minimum coverage of 40X. Assembly files consisting of highly fragmented contigs (> 500 contigs or N50 < 20K) or not complying with the species-specific quality criteria for the bacterial group will not be accepted. Submissions containing low quality assemblies may be entirely rejected.

The species-specific criteria can be accessed from the bacterial group’s home page by clicking on "Pathogen-specific quality criteria" or directly at the bottom of this page.

Please note that genomes obtained by Ion Torrent/Roche/454 will not be uploaded to the database, nor used to define new alleles.

NB. However, if you discover new MLST profiles only composed of already existing alleles, you can make a 'profile' submission type to define a new ST, no matter the assembly technology.

Illumina

Please note that, for Illumina, we only accept genomes that fit the following requirements :

• Minimum coverage depth of 40X

Oxford Nanopore

For ONT data, two levels of requirements apply: mandatory criteria that will result in automatic rejection if not met, and recommended parameters that ensure the best assembly quality.

❌ Mandatory requirements — submissions not meeting these criteria will be automatically rejected

• Sequencing must have been performed using Oxford Nanopore Technologies R10.4.1 chemistry or higher (Rapid Barcoding Kit V14 / Ligation Sequencing Kit V14 or higher)
• Raw ONT data must have been basecalled using SUP (Super-Accurate) mode — assemblies basecalled with other modes (e.g. HAC, FAST) will not be accepted

⚠️ The sequencing kit and basecalling information are mandatory. Any submission lacking these details will not be processed, regardless of assembly quality.

✅ Recommended parameters for high-quality assemblies

The following parameters represent the minimum recommended versions. Using more recent software versions is accepted and encouraged:

• Raw ONT data basecalled with Dorado SUP (with the latest SUP model e.g. dna_r10.4.1_e8.2_400bps_sup @v5.2.0, find the lastest model here)
• Assembled with nanodna if possible or with Flye (v2.9.5 or higher)
• Minimum coverage depth of 50X
• Dorado summary file on SAM/BAM files produced by the dorado basecaller

🏢 Third-party sequencing or assembly

If your data was sequenced and/or assembled by a third-party company or service provider (i.e. not by the submitter directly), please make sure to contact them in advance to retrieve all the information listed above (chemistry version, kit, basecalling mode and model, assembly software and version, coverage depth). This information should be provided in the submission messages section. Submissions lacking these details will not be processed.

Please provide information on the sequencing and assembly technologies used in the submission messages section.

Quality criteria for specific bacterial groups

🦠 Organism	Illumina	Oxford Nanopore	Quality Criteria
Bordetella	✅	✅	Quality Criteria
Corynebacterium diphtheriae complex	✅	✅	Quality Criteria
Elizabethkingia	✅	❌	Quality Criteria
Escherichia coli	✅	❌	Quality Criteria
Klebsiella pneumoniae species complex	✅	✅	Quality Criteria
Leptospira	✅	❌	Quality Criteria
Listeria monocytogenes	✅	✅	Quality Criteria
Staphylococcus epidermidis	✅	❌	Quality Criteria