Submissions:

Please submit all data (isolate’s information and sequence data) for allele and types definitions through your BIGSdb-Pasteur submitter account.

By default, all submissions remain private under the submitter’s project(s). Isolates can be made public at any time, upon the submitter's request.

Users are requested to submit only high-quality assemblies, generated from pure cultures sequenced at a minimum coverage of 40X. Assembly files consisting of highly fragmented contigs (>400 contigs or N50<20K) or presenting a cumulative contigs length outside the typical range of Listeria (2.5-3.5 Mb) will not be accepted. Submissions containing low quality assemblies may be entirely rejected.

Once you are logged in to the Isolates database, go to SUBMISSIONS to access the submission panel. Choose genomes to upload the assembly files (closed or draft genomes in FASTA format) and isolate information sheet (use the template available there). In the template, only minimal metadata is requested. Typing info fields (lineage, MLST/cgMLST fields or alleles) are reserved to the curators (please do not fill them). The submission process is straightforward and takes only a few minutes.

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).

We encourage submission of all isolates of your studies, so that the database would be as representative of the natural populations as possible. Thus, please do not restrict yourself to submitting only isolates that represent new profiles: isolates with already known MLST types are valuable as well.

Please note that only submissions made through the Isolates database/SUBMISSIONS/genomes are considered for new alleles and profiles assignations.

Results are typically available in <24h for small batches or several days for larger batches (hundreds of genomes). Given high number of submissions, priority is given to private data.

Acknowledgments:

We appreciate if you can recognize our efforts in the acknowledgments section of your publications:

“We thank the Institut Pasteur teams for the curation and maintenance of BIGSdb-Pasteur databases at http://bigsdb.pasteur.fr/”.