Can this workflow process single-end sequencing data?

[hyzhou1990]

Thanks for your wonderful jobs! It can process pair end sequencing data well.

I wonder if this workflow could process data of single-end sequencing.

[florianzwagemaker]

Hi hyzhou1990!

Glad to hear the workflow is working well for your paired-end sequencing data!

SARS2seq is also able to process single-end sequencing data, but this depends on the sequencing platform that was used.
Single-end sequencing data is supported for the Iontorrent and Nanopore sequencing platforms, for Illumina data only paired-end sequencing data is supported.

If you are trying to process Illumina single-end sequencing data then you can maybe try to run the workflow with in the "iontorrent" platform instead of Illumina. The Illumina and Iontorrent mode share a lot of analysis settings during the workflow so there's a good chance this works depending on your data.

If you have another type of single-end sequencing data could you then maybe share what kind of data this is? With some more information i can maybe look into a better solution for you.

[hyzhou1990]

Thanks for your detailed reply. I think you have solved my problem. My data was produced on an illumina platform and I will follow your suggestion to try the "iontorrent" workflow.