hifiasm

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hap1 and hap2 generated from different versions are of different sizes

2

The crop genome is inbred diploid. Estimate genome size is 1.2 Gb. v0.15 output: primary--1.12Gb, hap1-- 1.03Gb, hap2--1.02Gb; v0.19 output: primary--1.1Gb, hap1--831Mb, hap2--470Mb. Default parameter settings were used. Could you...

xzhoubayer

I'm trying to assemble a tetraploïd genome with hifiasm 0.19.8 using the --n-hap 4 option. But when I check the assembly kmer content there are many missing kmers even when...

chklopp

My assembled genome species has a genome size of 2.6 Gb with extremely rich simple repeat sequences. I assembled it using 21x Hifi, trio data, and 15x ONT (>40k) data,...

YouxinZhao

possible regression in using HiC reads in --h1 --h2

5

Version hifiasm_0.19.8-r603 using --h1 --h2 is stopping at a Partition step after the hic.p_ctg gfa is written. Last version that we had run that worked for us was hifiasm_0.19.5-r590 so...

jbh-cas

Hifi + hiC assembly stuck at max_n_chain to 100

4

I have a large genome (~5GB) with N50 ~3Mb, and 30X of Hi-C coverage (uniquely mapped reads) The assembly is stuck at for two days. I moved to assemble the...

gushiro

adapterLen mismatch

1

Hello, I am trying to add phasing information to a previously unphased assembly of HG00733 using the HGSVC data. I am using hifiasm v0.19.6 to add phasing information after the...

wharvey31

Segfault when incorporating HiC data

1

I ran into a funny issue when assembling a 30+ GB genome using data from an trio-phased interspecific F1. The assembly of HiFi data works fine, but the assembly dies...

jeramiahsmith

SegFault during GFA output stage

2

Sample: human with ~31x coverage. Unfortunately, the data is protected so cannot be shared. I'm sorry. If you have time to guide us how to debug, I'd appreciate that! Thanks,...

SHuang-Broad

Feature request: Separate hifiasm into stages

10

Hi, Is it possible to separate hifiasm into stages (e.g. separating the read-error correction step and the phased string graph generation step)? The application that initially led us to ask...

SHuang-Broad

--n-hap 3 does not give three haploid genomes

1

I have a genome that BUSCO, genomescope and natural history suggest is triploid. When I use --n-hap 3 however, I only get hap1 and hap2 and the assembly is almost...

tallnuttrbgv