hifiasm

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overlap parameter

2

I am trying to assemble the haplotype genome. We have high depth HiFi data of about 150×, which we want to assemble through Hifiasm software and improve the accuracy by...

tianjio

Hi, I found that the contig number of haplotype 1 from hifiasm are always large contig number of haplotype 2. What causes this? Is there any explanation in the article...

Chenglin20170390

larger assembly size than kmer estimation genome size

2

Hi, I estimated the genome size with HiFi data, the estimated genome size is 328Mb with 1.02% hetorozygosity:  I assembled the primary genome and phased genome with HiC data...

leon945945

Reads has been loaded. Loading ma_hit_ts from disk... ma_hit_ts has been read. Loading ma_hit_ts from disk... ma_hit_ts has been read. [M::ha_assemble::422.189*0.88] ==> loaded corrected reads and overlaps from disk [M::ha_opt_update_cov_min]...

dabitz

Add discussion - polyploid genomes

1

Hi, this is not really an issue - could I suggest the author adds a discussion page? There is much interest in assembling phased polyploids at the moment, especially in...

tallnuttrbgv

ERROR6 and others probably no warning

6

Dear all, after using hifiasm for a long time, we recently observed strange behavior for one assembly in particular. When running hifiasm 0.19.8, the tool returns ERROR6 and other messages:...

schellt

Hi I tied to assemble a bacterial genome (about 3MB) from PacBio Sequel II HiFi reads (about 1 million reads, mean length 6500bp) using a work station with 16 threads...

microbiota2022

Hi, I have just used the hifiasm tool to generate a few assemblies (it's great) I was just wondering if the position of the -l0 flag in the code affects...

Rhia15

output files empty

4

Hey! Just ran HiFiAsm on my yeast data, and things got weird. Got nothin' but empty files back, except for those .bin files. Attached the .log file in case it...

kathbarros

Aborted on recalculate_window_advance()

2

Hello hifiasm team, I am trying to use hifiasm on simulated HiFi and Nanopore reads (so both datasets are haploid, since they came from published genome assemblies. As I read...

jwalewski