How to align both long and paired end short reads using vg

[nathanLauHKGI]

Hi there

This is another clarification question:

Is there a recommended way align both long and paired end short reads using vg?

[jeizenga]

Paired-end short reads are fully supported. To access the paired-end features, you can use two -f arguments to provide the R1 and R2 reads. We are currently developing long-read alignment support, but these features are still experimental. You shouldn't yet expect a consistent interface or consistent performance for giraffe's long-read mapping.