This tool allows users to generate a sequencing quality-control report by aligning sequencing data against reference sequences, computing coverage, and identifying variants in sequenced samples.

Input: Sequencing data (FASTQ files)

Output: A set of quality-control reports, each corresponding to a sequenced sample.

You can find the Sequencing Quality Control tool under Tools > Tool Library. Click ‘Launch Tool’ to start using the tool.

The tool will walk you through several steps. You need to complete each step before proceeding to the next. After completing a step, the completed step mark (circle) will turn green with a checkmark. You can always use the ‘previous’ button to go back to any previous step.

  1. Select Sequencing Data. The tool will assume you already have samples in the system that you have sent out for sequencing. Those samples should be represented in your database with entries for sequence, material, sample, and aliquot. The demo lab should have two test data for this purpose with the sample names "SeqQCTestSample_1" and "SeqQCTestSample_2". Search the aliquot data to make sure this data is present.

If they are not present, you will need to do a plate upload with information about the plate name and associated Genbank files that contain information about the expected sequence. Inventory > Plates > Upload. You can download the Plate upload csv and complete it as shown.

Once the aliquots are represented, you can start the Sequence QC Tool, and upload your FASTQ files which contain information about the measured sequence. Your FASTQ files must be named such that the aliquot name appears in the FASTQ filename in the following way:

Aliquot_{{aliquot ID}}_R1_{{any text you wish}}.fastq

Aliquot_{{aliquot ID}}_R2_{{any text you wish}}.fastq

The file names start with "Aliquot_", followed by the aliquot ID, followed by "_R1_" which identifies the sequencing run, followed by any additional naming text, we suggest the sample name for easy identification of the file. In our example we will upload four files, two sequencing runs for each sample:

Aliquot_1877_R1_SeqQCTestSample_1.fastq

Aliquot_1877_R2_SeqQCTestSample_1.fastq

Aliquot_1878_R1_SeqQCTestSample_2.fastq

Aliquot_1878_R2_SeqQCTestSample_2.fastq

At the parameter setup step, you can just keep the default settings for now.

The tool will upload the FASTQ files and generate a QC report for you.

Click to open the reports table...

When the reports have finished processing you can open them for inspection. You can also record the sequence as QC'ed if you approve of the quality.

Deviations between what was expected (REF) and what was measured (ALT) are shown in both graphical and tabular form.

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