Sequence Association Tool

Update the sequence information for existing samples

Written by Siobhan Davis
Updated over a week ago

This tool allows users to update the sequence information for existing plate wells or tubes via a CSV/Excel file or a data table. It is required that the plates or tube racks specified in the CSV or data table must exist in inventory. This tool is generally used after the ‘Colony Picking Feedback’ tool.

Input: CSV or Excel files or data tables describing which aliquots need to be updated with sequence information.

Output: Plates with aliquots updated with sequence information.

You can find more detailed definitions of the terms mentioned in this article in the glossary.

Prerequisite: It is required that each aliquot being updated with sequence information must be assigned to a container and the container must have a barcode. It is also required that the sample to which the aliquot belongs must have the type of ‘Isolated Sample’.

You can find the ‘Sequence Association’ tool under Tools > Tool Library. Click ‘Launch Tool’ to start using the tool. This tool consists of only one step, which is to upload or select sequence association schema.

1. Select Sequence Association Schema: Select a sequence association schema from the ‘Data Tables’ inventory or upload a schema in either CSV or Excel format.

1.a. Select Data Table: With the ‘Select Data Table’ option, you need to upload a data table of type ‘Sequence Association Schema’ ahead of time by going to Data > Data Tables > Upload > Upload Table. You then can select a pooling schema from all the data tables of type ‘Pooling Schema’ in the ‘Data Tables’ inventory. Note that if you choose the schema using this option, you can’t associate a sequence file with the existing aliquots because the ‘Data Tables’ upload does not support zipping sequence files with a CSV or Excel file.

1.b. Upload Pool Schema: Turn on the toggle button and select a schema file in CSV or Excel format from your local computer. The template for the sequence association schema is shown below. The required fields are ‘Barcode’. Other fields are either optional (recommended) or conditionally required depending on the availability of one or more other fields.

Barcode: the barcode of the container to which the aliquots to be updated with sequence information is assigned.

Position: if the provided barcode belongs to a plate or a tube rack, the position is conditionally required to provide the explicit position of the aliquot. Eg. A1, A2, etc.

Sequence Type: this field is (conditionally) required if ‘Sequence File’ is not provided (only sequence text is provided) or if the provided sequence file (eg. Fasta file) does not include this information.

Sequence Name: this optional field allows users to specify a name for the sequence to be associated with an aliquot. If a sequence file is provided, the sequence name can be extracted from the file. If a sequence file is not provided, and you do not specify a sequence name and a sequence name prefix, the sequence will have the name ‘Untitled Sequence’ in the ‘DNA Sequences’ library.

Sequence Name Prefix: this optional field allows users to specify a prefix for the sequence name. The system will generate a unique numerical ID for each sequence and append the ID to the prefix and use that as the name of the sequence.

Sequence: A nucleotide sequence. This is required if the sequence file is not provided.

Sequence File: Genbank or Fasta sequence file name (including the file extension). This is required if the sequence is not provided. If a sequence file is provided, you should zip the sequence file with the CSV/Excel file before the upload.

Note: If the sequence file is a Genbank file that has multiple sequence entries, you should use the ‘Sequence Name’ field to list the Accession number from the Genbank file to let the system know which sequence from the file is associated with which aliquot.

Once the sequence association schema is uploaded, users can review the schema before clicking ‘Submit’. If the system detects any invalid information (eg. barcodes do not exist in inventory, aliquots do not have any materials, an aliquot is already associated with another sequence, or you forget to include the sequence file), warnings will be displayed in the form of red info icons next to problematic entries. These warnings need to be resolved before completing the tool.

Once all the warnings are resolved, click ‘Submit’ to complete the tool. You will then be notified that the sequence association is completed and there is a link to the destination container(s) that store(s) the aliquots that are now associated with sequence information.

Open the plate record view and click on one of the aliquots to open the aliquot record view. As shown below, the aliquot record view now is updated with sequence information that is missing from the record view before sequence association. Before sequence association, there is material link to the aliquot, but after sequence association, new material is created and linked to the aliquot.

View of Aliquot 3288 before ‘Sequence Association’:

View of Aliquot 3288 after ‘Sequence Association’:

If you click on the sample link, you should see that the sample now has a status updated from ‘Unvalidated’ to ‘Valid’.

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