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philres / ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
MIT License
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Parameter for corrected PacBio reads ? #52

Open ptranvan opened 6 years ago

ptranvan commented 6 years ago

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 commented 6 years ago

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 commented 5 years ago

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