Submitting Samples

The Nomenclature Server ( provides a global nomenclature for stable public cgMLST schemes, i.e. for Task Template that were downloaded from the Task Template Sphere. If Samples are using those downloaded Task Templates they can be submitted to However, if a Sample has new alleles that are not known at, then the Sample must be submitted with some minimum data to retrieve newly assigned allele types for them. Otherwise the new alleles are treated as missing data in distance calculation.

Button16 Important.png Important: If no submission of any data is wanted or allowed, then only local Task Templates must be used. Samples that are using only local Task Templates will not and cannot be submitted to Local Task Templates can be defined using the cgMLST Target Definer, or by converting public Task Templates into local ones.

The submission of a Sample requires the following minimum data:

  • Sample ID (alternatively Alias ID or do not submit and use Ridom ID)
  • Submitter Info (not shown public)
  • Submission Date (only year is shown public)
  • MLST Sequence Type (ST)
  • Core and accessory genome MLST allelic profiles
  • cgMLST Cluster Type (CT, returned from
  • Percentage of Good cgMLST Targets
  • Genus
  • Species

The amount of additional metadata that should be submitted can be defined in the Submission Anonymization Filter.

Submission to is only possible if the Sample has in the cgMLST scheme at least 90% of good targets (i.e., targets passed the QC procedure and have therefore a green or yellow smiley). Allele types are only received for the good targets (green or yellow smiley). During the first submission, the user must register once with basic contact information. This information can later be modified using the menu function Options | User Settings. The submitter contact information is not public shown on, but it will be used to forward incoming requests about submitted Samples.

Except for the submitter information and exact submission date any submitted data is immediately made publicly available on A unique serial number is assigned to the sample, and stored back as Ridom ID in the local database. This number is also shown as link in the upper right corner of the Sample Overview. This Ridom ID link can be used to directly access the public web page of the submitted Sample and to control the data that was submitted (e.g. RID002433).

There are two different ways in SeqSphere+ to submit Samples to

Manual Submission

Submission Preview dialog shown for manual submission to
  • Step 1: Load the Sample(s) into the workspace using the menu function File | Search Samples.
  • Step 2: Invoke the menu function File | Assign or Submit new Alleles and select all Samples that should be submitted.
  • Step 3: The Submission Anonymization Filter dialog is shown to define which fields should be submitted. The last used setting is kept.
  • Step 4: Finally the Submission Preview dialog is shown with the filtered data that will be submitted. The data can now be controlled and modified just before sending it. When the dialog is confirmed, the shown data is send to

Submission via Pipeline

If Samples are imported through a pipeline, it can be configured in the Submission part of the Pipeline Script that the Samples are submitted to The Submission Anonymization Filter settings are defined for each pipeline script.

In contrast to the manual submission, the pipeline submission does not show a preview dialog before the samples are submitted, because all pipeline processing runs in an automatized way. Therefore, the button Preview Epi Data can be used to show the potentially submitted epi data of the matching samples that already exist in the SeqSphere+ server database.

Resubmitting Samples

If a Sample that was already submitted is submitted again, then the data at is immediately updated. Fields that are filtered out or set to empty in the re-submission are immediately removed from

The procedure for re-submitting Samples is the same as described above in the manual submission section.

Filtering Metadata for Submission

The level of metadata that should be submitted can be defined in the Submission Anonymization Filter that is shown in a dialog before a manual submission is confirmed. Also in a pipeline script the Submission Anonymization Filter settings can be configured if automatic submission is selected.

New epidemiological fields that are created by the user are never submitted.

Potentially the following metadata is submitted to and shown on the public website. Unless the fields are mandatory, they can be excluded from submission (Do Not Submit). For place and time information additionally the level of detail can be set. The table shows the default settings for a new installation of a SeqSphere+ Client.

Submission Info
Submitter Info Submit (mandatory, not public)
Submission Date Submit (mandatory, only year is public)
Sample Ridom ID Submit (generated by
Genotyping Result
MLST ST Submit (mandatory)
cgMLST/Acc. Allelic Profile Submit (mandatory)
cgMLST Cluster Type Submit (mandatory)
Perc. Good cgMLST Targets Submit (mandatory)
Sequence Data
Assembly Contigs (FASTA) Submit
Epi Basic
Sample ID Submit
Alias ID Do Not Submit (alternative for Sample ID)
Collection Date Submit
Epi Source
Country of Isolation Submit
State of Isolation Submit
City of Isolation Submit
Source Type Submit
Host Submit
Host Age (years) Submit
Host Sex Submit
Host Disease Submit
Isolation Source Submit
Epi Characteristic
Genus Submit (mandatory)
Species Submit (mandatory)
Strain Submit
Genotype Submit
Serotype Submit
Pathotype Submit
Identification Method Submit
Identification Kit Vendor Submit
Culture Collection Submit
PubMed ID(s) Submit
Nuccleotide Accession(s) Submit
Experiment Accession Submit
Sample Accession Submit
StudyAccession Submit
Imported from EBI/NCBI1) Submit (mandatory)
Epi Species Specific
PFGE Pattern(s) Submit
Epi Species Specific (only for MTBC)
Spoligo Submit
MIRU 15-9 Type Submit
MIRU Lineage Submit
Gagneux Lineage Submit
Laboratory Procedure Details
Nucleic Acid Extraction Submit
Library Source Submit
Library Strategy Submit
Library Selection Submit
Library Construction Method Submit
Library Amplification Method Submit
Sequencing Protocol Submit
Library Insert Size Submit
Sequencing Length Submit
Sequencing Vendor Submit
Sequencing Platform Submit
Assembly Procedure Details
Assembly Pre-processing Submit
Assembly Type Submit
Mapping Reference Genome Submit
Assembler Submit
Assembler Version Submit
Assembler Parameters Submit
Read Statistics
Avg. Coverage (Unassembled) Submit
Avg. Read Length (Unassembled) Submit
Avg. Read Length (Processed, Unassembled) Submit
Assembly Statistics
Contig Count (Assembled) Submit
N50 (Assembled) Submit
Consensus Base Count (Assembled) Submit
Avg. Coverage (Assembled) Submit
Genome Status1) Submit (mandatory)

1) The fields Imported from EBI/NCBI and Genome Status are automatically filled if the data was imported from NCBI Genomes or SRA. Imported from EBI/NCBI can be true or false. The Genome Status can have one of the following values: Complete Genome, Chromosome, Scaffold, Contig, or SRA.