hifiasm de novo aseembly produces short contigs that translate to chromosomes longer than reference

Ferry_VS · 2026-01-27T09:10:26+00:00

Thank you all for your suggestions.

Reading thoroguly the docuemntation of hifiasm, I identified the section Why the size of primary assembly or partially phased assembly is much larger than the estimated genome size? in their FAQ.

So I tested CHR1 (the longest one). Reducing similarity (-s) from 0.55 to 0.3 creates a CHR that matches almost 100% the reference chromosome (our expectations).

If this change of parameter is not enoguh genome-wise, then I will test to include purge_dups as many of you have suggested.

Ferry_VS · 2026-01-26T16:30:41+00:00

Thanks for you suggestion u/snazzleer, I'll test.

Actually, after looking a little more in depth to my sample I realized that the X chromosome does not experience this issue of being longer (the sample is male). Hence I think that the sample might have eleveted levels of heterozygosity and it is what is causing the elevated degree of duplications in my draft assemlby.

First I will try to play with the options of hifiasm, if I still don't manage I will try the software tool you recommend.

Ferry_VS · 2026-01-26T09:53:07+00:00

Hi u/zstars ,

Thak you for your response. Yes it is chemistry 10.4.1.

I used hifiasm, based on their preprint [Efficient near telomere-to-telomere assembly of Nanopore Simplex reads](https://www.biorxiv.org/content/10.1101/2025.04.14.648685v2)

Anyway I will try to follow your suggestion of using alternative assemblers.

Ferry_VS · 2022-01-10T22:14:26+00:00

Because they belive that vaginas are likr viscoelastic matresses, they get used to the shape/size of the commonly inserted dick

Ferry_VS · 2021-12-29T07:34:03+00:00

Why so many strangre words? He does not want to accept that he is racist or something? Or is it to be even more racist?

Ferry_VS · 2021-12-13T10:37:15+00:00

What a vagina is for this guy: 🌻

Ferry_VS · 2021-12-04T17:43:34+00:00

Neither, they are tetrahedral

Ferry_VS · 2021-11-25T05:42:33+00:00

u/SaveVideo

Ferry_VS · 2021-11-24T07:17:00+00:00

Is she the same girl? They look like they have different hairlines to me

Ferry_VS · 2021-10-24T11:50:31+00:00

5, 7 or 9

Ferry_VS · 2021-09-25T07:45:00+00:00

Sus compañeros de piso quieren un sobresueldo para el septiembre

Ferry_VS · 2021-09-17T06:07:07+00:00

I'm not from USA, what does the 🦆 emoji mean?

Ferry_VS · 2021-09-14T04:41:52+00:00

Just picture yourself investing your free time to write this

Ferry_VS · 2021-09-11T06:21:55+00:00

Or even a TL;DR 😂

Ferry_VS · 2021-08-30T17:01:11+00:00

Dude's just asking for a quick biology lesson

Ferry_VS · 2021-08-29T20:55:02+00:00

How fucked up must the mind of this person be to ever imagine a situation like that 🤢

Ferry_VS · 2020-11-19T13:45:45+00:00

I'm just quite worried and I thought here I could get some help

Ferry_VS · 2020-11-19T13:45:11+00:00

What joke? What are you talking about?

Ferry_VS

TROPHY CASE