Amplicon Sequencing alignment report

Quentin Aeberli

• June 02, 2021 14:01
• Edited

Hi! We routinely use a homemade workflow which creates alignments from amplicon read type Ilumina and calls SNP on these alignments. I sought several paths to automatically summarize and group the alignment results in a report of type .csv. Typically containing: number of reads-reference sequence-SNP-SNP position…. All information needed are generated by the workflow and stored in the alignment files. Having typically 150-300 alignments created by run we seek to automatically generate a summary report. Did I miss an easy way to do this without coding in Java? Is there a possibility to pay for such a plugin to be developed?

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  Hilary Miller

  • June 02, 2021 23:33

  Hi Quentin

  If you are using the same reference sequence it should be possible to get all of the SNP tracks on the one reference document, and then you can just export all of the SNP calls from all of the tracks in one csv document.  I'm not sure if you'll be able to configure that as part of your workflow or if you'll need to do it "manually" after the workflow has run.  If you can contact us directly on support@geneious.com with an example of your workflow we can take a look.  

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