Used in production?

[colindaven]

Hello,

I have been running into problems mapping with vg on plant pangenomes. I would like to speed up the process.

Is reference_flow being used anywhere in production yet, or it still at the idea and proof of concept stage ?

Thanks,
Colin

[milkschen]

Hello @colindaven,

Reference flow was tested for pipelines such as mapping reads with bowtie2 and calling variants with GATK. A bwa_mem-gatk pipeline also worked, but required some customization of the workflow.

We have been recently working on a migration to replace the leviosam lift-over software with leviosam2, which would reduce some local lift-over errors and improve speed. I'm happy to send you an update when that's available.