Whole genome sequencing data requirements
Users are requested to submit only high-quality assemblies, generated from pure cultures and sequenced at a minimum coverage of 40X, that comply with the KlebNET-GSP quality criteria. Assembly files consisting of highly fragmented contigs (> 500 contigs or N50 < 20K) or presenting a cumulative contigs length outside the typical range of the Kp species complex (~ 4.6 - 6.4 Mbp) will not be accepted. Submissions containing low quality assemblies may be entirely rejected.
⚠️ NB. For quality purposes, we only accept assemblies either generated from high quality short-reads, combining both short and long reads (hybrid assemblies) or Oxford Nanopore (check conditions below). Please note that genomes obtained by Ion Torrent/Roche/454 will not be uploaded to the database, nor used to define new alleles. 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.
Please refer to the assembly metrics below:
| Species | Size of genome | Number of contigs | C+G% | Coverage |
|---|---|---|---|---|
| K.pneumoniae | 4 700 000 - 6 300 000 | ≤ 500 | 56.1 - 58.1 | >= 40 |
| K. quasipneumoniae | 4 900 000 - 6 100 000 | ≤ 500 | 56.7 - 58.4 | >= 40 |
| K. quasivariicola | 5 400 000 - 6 100 000 | ≤ 500 | 56.1 - 57.4 | >= 40 |
| K. variicola | 5 200 000 - 6 200 000 | ≤ 500 | 56.5 - 57.8 | >= 40 |
Nanopore submissions
Please note that, for ONT, we only accept the genomes that fit the following requirements :
- Oxford Nanopore Technologies R10.4.1 - Rapid Barcoding 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 50×
- 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.