The BIGSdb website is implementing new settings regarding data access. Data curated in 2025 (and later) will not be accessible for anonymous (non-logged-in users). If you wish to have access to data curated in 2025 and beyond, please register on the platform and login when using it. Note that access via the application programming interface (API) will also require authentication to access recent data (API authentication help link).
To ensure a smooth transition, anonymous data access will be periodically closed and opened from 1st October 2024 until the end of the year. For detailed planning, please follow this link.
On 1st January 2025, registration will be permanently mandatory to access data curated after the 31st of December 2024.
Please contact us if you have any questions.
Quality criteria for accepting whole genome sequencing data
Users are requested to submit only high-quality assemblies, generated from pure cultures sequenced at a minimum coverage of 40X. Assembly files consisting of high numbers of contigs (> 500), presenting a cumulative contigs length outside the typical range of Bordetella species (~ 3.2 – 6 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:
| Species | Size of genome | Number of contigs | C+G% | Coverage |
|---|---|---|---|---|
| B. bronchiseptica | 5000000 - 5600000 | ≤ 500 | 67.8 - 68.7 | >= 40 |
| B. holmesii | 3400000 - 3800000 | ≤ 500 | 62.6 - 62.9 | >= 40 |
| B. parapertussis | 4400000 - 4900000 | ≤ 500 | 67.7 - 68.2 | >= 40 |
| B. pertussis | 3300000 - 4100000 | ≤ 500 | 67.1 - 68.1 | >= 40 |
| other | 3700000 - 5900000 | ≤ 500 | 59.4 - 69 | >= 40 |