the detail steps of StrainScan

[chaoyanggu]

Dear Professor,
We are using StrainScan to build a k-mer index based on our custom database, and the pipeline can identify which samples are polyclonal and predicted their corresponding strain origins. However, the current workflow lacks too many intermediate files and filtering steps. Therefore, we would like to obtain detailed information about the running steps, such as their variant sites and the read origins. We believe it would significantly enhance the software's flexibility for advanced users and facilitate deeper understanding of the algorithm's core mechanisms.
This capability would be particularly valuable for our research, as we're working with pre-processed sequencing data. Your guidance on whether this approach is technically feasible would be immensely appreciated.
Thank you for your reply.
Best regards

[liaoherui]

Hi Chaoyang,

Thanks for using StrainScan, and sorry for the late reply!

More details about the method can be found in our paper. The functions you mentioned—such as identifying variant sites and read origins—are very interesting! While I haven’t had time to work on these features due to other ongoing projects, I do plan to develop a new strain-level identification tool that incorporates them. Feel free to reach out if you’d like to discuss further!

And yes, StrainScan can be directly applied to pre-processed sequencing data. In our real-world dataset experiments, we used pre-processed data.

Feel free to let me know if you have more requirements or problems!

Best,
Herui