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Organism Specific

Submitting Data
    Sequence Types
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    Next-gen data


Policy Document

Submitting Data

The MLST website provides the official allele and ST designations and assignments of new alleles and STs can only be made by the curators and/or the webmaster.


New Allele Sequences

For any novel allele sequence we require both the forward and reverse trace files for quality checking prior to assignment of a new allele number. Data should be sent to the curator of the relevant database who will be responsible for the correct assignment of alleles. In case of disagreement, the allele may be re-sequenced by the curating laboratory.  Once assigned the new alleles are added to the database. The email of the curators can be found on the homepage of each MLST species website.

For previously known alleles, the responsibility of correct allele assignment rests with the user.

New Sequence Types

The allelic profiles of novel STs should be sent to the curator of the relevant MLST database along with the details of at least one isolate of the novel ST that will be entered in the database. An Excel template for submitting the details of isolates of new STs to the curator must be used and is available from the front page of the relevant MLSTspecies website (see next paragraph).

Please note that new allelic profiles will only be assigned their official ST numbers on submission of the details of at least one isolate of the new ST for entry into the MLST database.

We strongly urge the submission of isolates of known STs together with the details of the isolates as submitting only novel STs introduces strong bias into the databases.


Epidemiological data for Isolates

On the frontpage of each MLST database, a link to an Excel Template for data submission can be found. This contains all the column headings for epidemiological data indicating those that are required and those that are optional.

We strongly encourage you to submit as much epidemiological data as you can and for as many isolates as you can. MLST databases provide better insight into the epidemiology of a species as more data are submitted.

To submit your isolate data please email the completed Excel sheet to the curator of the relevant MLST database.


Next generation Sequence Data

As newer sequencing technologies become more widely available we are receiving requests to accept alleles generated using these technologies. As such, we provide a minuimum criteria for coverage and quality for each method as follows:


We require the sequences of each MLST locus, preferably in FASTQ format, so that we can assess the quality of coverage before assigning new allele numbers.

Our minimum requirement is 30X coverage across each gene fragment with a quality of XX


Brian: we could indicate that data should first be checked within Artemis using the BAM viewer - or indeed that we require BAM files rather than FASTQ

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