Missing all-vs-all function in Minimap2

Healthcare & Life Sciences Parabricks
1

Hello, I am trying to do all vs all mapping of ONT long reads but found that “-x ava-ont” is not implemented in 4.3.2-1. Is there any equivalent combination of parameters that can achieve the same function? Thanks!

2

Hi @sh0rt2l0ng,

There is currently no equivalent flag for that in the Parabricks implementation. I’ve sent this feedback to the engineering team so they can discuss about potentially adding it in the future.

Thank you

1 Like
3

Hi @gburnett ,

Thanks for the reply! Could you please have dev team also consider “-y” option in minimap2 which transfers comments in fastq read id into bam? That would be very helpful too.

4

I just submitted the feature request and added that. Thank you for letting us know that this addition would be helpful for you.

1 Like