search

mehrdadbakhtiari / adVNTR

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
http://advntr.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
39 stars 15 forks source link

trained VNTR models for Nanopore data #33

Open nbargues opened 4 years ago

nbargues commented 4 years ago

Hi, when I download vntr_data_recommended_loci.zip , there are two files ( illumina and pacbio ). If I have Nanopore data, can I choose the pacbio file or do you have a specific nanopore file that I can find ?

mehrdadbakhtiari commented 4 years ago

Hi, we haven't extensively tested and measured the accuracy on Nanopore data. However, you can use the file related to pacbio and it should work reasonably well. Although they have relatively different error profile, given the long read in both there can be long run of well aligned basepairs so you can try to run the tool with pacbio data and --pacbio argument.

nbargues commented 4 years ago

Thanks for the response. So you suggest to use --pacbio argument, even if I have Nanopore data and that you have a --nanopore argument ?

mehrdadbakhtiari commented 4 years ago

Yes, --nanopore is not fully tested and current version won't let the code run. But I assume by pacbio parameters you can still get a relatively good results and it worth trying.