Parameter for corrected PacBio reads ?

[ptranvan]

Hi,

What would be your recommended parameters to map corrected pacbio reads (after 1 step of canu for example) against a genome ?

This will be used for inversion detection (with sniffles or/and npinv)

Thanks.

[fritzsedlazeck]

I would still use the default pacbio parameters. The score function is taking the error pattern into account, but not the frequency of the errors. However, please report back as we did not make a ton of experiments about that. Thanks Fritz

[sjin09]

Hello @ptranvan and @fritzsedlazeck

I was wondering if you guys were able to find a set of best parameters for either aligning the error-corrected reads or the new HiFi reads. We are assessing the alignment results from nglmr and minimap2 and how the alignment results influence germline mutation detection using longshot and/or deepvariant.

Many thanks, Sangjin