some problem occurs when evaluating the data of na12878 chromosome 21 about helen HOT 4 CLOSED

Hello @huangnengCSU ,

I have a few questions:

1. What guppy version are you using? I see you are using guppy 235 model file for MP but for HELEN you are using guppy 344 models, do you know which version of the basecaller are you using?

2. How did you generate your assembly? What are the pomoxis numbers for the raw assembly?

3. I see you are using hg38 as the "truth", that will have some potential issues, especially in the centromeric, seg-dups and SVs of NA12878. HG38 is not truely representative on any "one" sample. I would highly recommend using the BED file provided by GIAB and pass that to pomoxis for a better assessment.

from helen.

To kishwarshafin
The raw data was basecalled with Albacore v2.3.4. The long reads assembler we used was Flye. And thank you for your advice about the reference.

neng

from helen.

@huangnengCSU ,

Albacore v234 is obsolete at this moment. We don't have a model to support that basecaller. There are publicly available data with the latest basecaller that you can use. If you have issues with the newest basecallers please let us know.

from helen.

To kishwarshafin
Thanks for answering the question, I will close the issue.

from helen.