The BIGSdb website Policy concerning the platform & data use agreement and the privacy notice of BIGSdb-Pasteur was updated on March 25, 2024. Please consult it before using the platform and the data.

The procedure for submitting data for curation were updated on Mai 03, 2024. Please consult them before making a new submission. If any questions, contact us.

Quality criteria for accepting whole genome sequencing data

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. Please note that new alleles and profiles will not be defined based on long-read sequence technology alone nor based on Ion Torrent/Roche/454, to avoid introducing artifact sequences in the database due to low accuracy sequencing. For typing purposes, we recommend using only assemblies either generated from high quality short-reads or combining both short and long reads (hybrid assemblies).

Please refer to the assembly metrics below:

SpeciesSize of genomeNumber of contigsC+G%Coverage
K.pneumoniae4700000 - 6300000≤ 50056.1 - 58.1>= 40
K. quasipneumoniae4900000 - 6100000≤ 50056.7 - 58.4>= 40
K. quasivariicola5400000 - 6100000≤ 50056.1 - 57.4>= 40
K. variicola5200000 - 6200000≤ 50056.5 - 57.8>= 40
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