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

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

• Oxford Nanopore Technologies R10.4.1 - Rapid Barcoding Kit V14 - Ligation Sequencing Kit V14
• 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

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

Quality criteria for specific bacterial groups