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

adNVTR using assembly-level data #50

Closed WeiYang-BAI closed 2 years ago

WeiYang-BAI commented 2 years ago

Hi,

Not an issue, I'm just wondering if adVNTR suits for assembly-level data generated from PacBio HiFi reads?

Thanks!

Jong-hun-Park commented 2 years ago

Hi @WeiYang-BAI ,

If you are referring to assembly sequence (a single sequence), adVNTR doesn't suit those data. adVNTR takes sequencing reads as input. As adVNTR estimates repeat counts based on the number of reads aligned to VNTR regions, a single sequence wouldn't output the correct genotype.

WeiYang-BAI commented 2 years ago

Thanks @Jong-hun-Park , got it.