DeNovoGBS, max k-mer size

NGSEP / NGSEPcore

NGSEP is an integrated framework for analysis of high throughput sequencing (HTS) reads. The main functionality of NGSEP is the variants detector, which allows to make integrated discovery and genotyping of Single Nucleotide Variants (SNVs), insertions, deletions, and genomic regions with copy number variation (CNVs).

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DeNovoGBS, max k-mer size #37

Closed MWSchmid closed 2 years ago

MWSchmid commented 3 years ago

Hi there

Thanks for the nice tool.

A question regarding the k-mer size in DeNovoGBS. I just tried increasing it to 101, but I get an error:

"The maximum k-mer size for this class is 31."

Is there a way to bypass this? Or is it pointless anyway to use k-mers larger than 31?

Best regards,

Marc

jduitama commented 2 years ago

Hi Marc

Thanks for your interest in our new function and my apologies for the late answer. Due to technical constraints with the algorithm design, we set the maximum k-mer size to 31. Larger values will significantly increase the memory consumption and are not likely to make an improvement in clustering or genotyping quality.

Best regards

Jorge