Integrating s-aligner into Illumina Basespace Sequence Hub

Accorging to Illumina this is BaseSpace Sequence Hub:

“BaseSpace Sequence Hub is a direct extension of your Illumina instruments. Encrypted data flow from the instrument into BaseSpace Sequence Hub, enabling you to manage and analyze your data easily with a curated set of analysis apps.”

Part of BaseSpace is the BaseSpace App store, in which third-parties can offer cloud services to BaseSpace customers. It’s like the Pkay Store for bioinformatics services.

You can, for example, order a de-novo genome assembly of your data, with the SPAdes software, just pushing a few buttons in the web platform. When the job is ready, you are notified by email. Some apps are free but most of them work with iCredits, a currency established by Illumina.

Very soon, Illumina customers will also be able to order similar jobs running s-aligner software. One App is already developed and tested. Now we just need to be authorized by Illumina to publish it.

This first App is for performing SARS-Cov-2 Variant Calling. We have already demonstrated the superior performance of s-aligner de-novo assembling SARS-Cov-2 genomes. Now we also demonstrate that de-novo assembling the virus has some advantages for Variant Calling. In case you don’t know, Variant Calling is the process by which the different variants of the virus are identified: Alpha, Beta, Delta… It’s also the way to trace the expansion of the virus, which is sometimes useful to prevent infections. All genome sequences submitted to GISAID pass through a Variant Calling process.

A Comparison of Performance for Different SARS-Cov-2 Sequencing ProtocolsMarch 1, 2021

The users of the App will just need to select a sample in their BaseSpace account and call the App. In a few minutes they will receive the variant-calling analysis, the consensus sequence, the de-novo assembly used for the variant-calling, and the Quast analysis of the de-novo assembly.

The advantages that I have found using this pipeline are:

  • Fewer false SNP’s
  • Detection of large indels that are missed by other popular pipelines

Now, it's all up to Illumina.

Of course, there is a relatively complex infrastructure behind to activate resources in the cloud for serving the jobs demanded in BaseSpace that maybe I will explain in another post.

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