Animal diversity feature requests

[McAllister-NOAA]

Hello! Thanks for this interesting tool. I have started testing use of it in our group at NOAA.

I am curious if you would be willing to add some parameters to control behaviors of the workflow:

1. A parameter to adjust the max contig length cutoff for mitochondrial sequences. While 16k might be the average length for an animal mitochondrial genome, there are many that are much longer. Including dungeness crab (39k) or some anenomes (80k). It would be nice to be able to use the tool regardless of the taxa of interest.
2. I'm wondering if it might be possible to implement a more taxa-dependent subsampling approach: taste the reads being supplied to determine a percentage of mitochondrial:nuclear reads. This could be a quick alignment step to a reference, or even just a quick step focused on the 12S/16S. Once that ratio is determined, then the subsampling parameter could be adjusted, potentially, to try to normalize the depth of the mitochondrial reads fed to the assembler. Just an idea!

Thanks!
Sean

[warrenlr]

Hello Sean, thank you for your suggestions and interest in mtGrasp.

Although mtGrasp was developed with animal MtG in mind, in principle, (1) should be relatively straightforward to implement, albeit testing may come with challenges on our end. We are currently unable to invest in the development/testing of additional features. I invite you to look at the open source code, should you be able to familiarize yourself with it.

Thank you,
Rene