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Inquiry Regarding Genome Assembly with ONT Data: Quality Comparisons and Recommendations

3

Dear Developer, I hope this message finds you well. First and foremost, I would like to extend my sincere gratitude for developing this remarkable software. It has been an invaluable...

Bank-tidy

Is such a k-mer plot normal?

2

As exmplified in [Issue10](https://github.com/chhylp123/hifiasm/issues/10) and [Issue49](https://github.com/chhylp123/hifiasm/issues/49), a good k-mer plot for heterozygous samples should have two peaks of which the smaller one is around the heterozygous read coverage and the...

YanCheer

Dear haoyu, I'm having some issues with reassembling with -5 arguments when running hifiasm, and the log file shows [M::ha_polybin_list::206185.837*4.95] created the hash table for read names, I get a...

lzux

Trio mode: hybrid in HIFI + parents in Illumina, resulting in assemblies with high duplication levels

6

Hello @chhylp123 I used hifiasm in trio binning mode using Illumina reads from the parents and HiFi reads from the hybrid. The resulting assemblies (hap1 and hap2) have high duplication...

carolhsb

Hi-C +HiFi sequencing run killed?

11

I am attempting to run a genome assembly and am running into an issue of the assembly getting killed at the very end. I saw some people having similar issues...

mabh5

After adjusting the parameters based on the information from the Hifiasm.log file, the issue of "phased assembly is much larger than the estimated genome size" still persists.

1

Hello, When assembling the genome of a species using HiFi data with hiFiasm, I encountered a peculiar situation. The genome size of my species is approximately 1.1 G. Following your...

xujialupaoli

Two hap are larger than survey and flow cytometry result

1

Dear Haoyu I have a species that survey and flow cytometry are 2.4G. This is PacBio data survey.  This is next generation sequence data survey.  But the hifiasm...

zhang144999

Hello! I'm getting error when running this command: ./hifiasm -o CHM13.asm -t32 -l0 CHM13-HiFi.fa.gz 2> CHM13.asm.log [ERROR] Cannot find the input read file: CHM13-HiFi.fa.gz I cant find the file CHM13-HiFi.fa.gz.

marcusgaspar

Assertion `((*q0l) == (*q1l)) && ((*t0l) == (*t1l)) && (err0 == err1)' failed

8

Hi, I am working on assembling a few genomes using both hifi and ont data. I was able to successfully generate one genome assembly, however the second has been unable...

erfrancoeur

Hello, dear developers, I encountered a strange problem. I appreciate your patience and assistance in providing me with any suggestions or ideas！I assembled a diploid genome using HiFi and Hic...

qdu-beep