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. Assembly files consisting of high numbers of contigs, or presenting a cumulative contigs length outside the typical range of the Corynebacterium diphtheriae species complex (~ 2.2 - 2.9 Mbp), will not be accepted.
NB. For quality purposes, we only accept assemblies either generated from high quality short-reads or combining both short and long reads (hybrid assemblies). Please note that genomes obtained using long-read sequence technology, or by Ion Torrent/Roche/454 will not be uploaded to the database, nor used to define new alleles. However, if using one of these assemblies you discover a new MLST profile(s) composed solely of existing alleles, you may make a 'profile' submission type to define a new ST.
Please refer to the assembly metrics below:
| Species | Size of genome | Number of contigs | C+G% | Coverage |
|---|---|---|---|---|
| C. diphtheriae | 2 300 000 - 2 600 000 | 20 - 90 | 53 - 54 | >= 40 |
| C. belfantii | 2 500 000 - 2 900 000 | 150 - 220 | 53 - 54 | >= 40 |
| C. rouxii | 2 200 000 - 2 500 000 | 20 - 55 | 53 - 54 | >= 40 |
| C. ulcerans & C. ramonii | 2 400 000 - 2 800 000 | 5 - 60 | 53 - 54 | >= 40 |
| C. pseudotuberculosis | 2 200 000 - 2 300 000 | 10 - 30 | 53 - 54 | >= 40 |