hifiasm
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chhylp123
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Hi, developers I have a question that I would like to ask you. I am assembling an allotetraploid genome (AABB), using the Hi-C mode and obtaining two haplotypes (hap1 and...
Hi, Would it be possible to add more checkpoints to prevent restarting the jobs if not enough memory or wall time has been provided? Many thanks for considering my request....
I am using the two haplotype assemblies of `hifiasm` (`fasta` files extracted from the`*hap*.p_ctg.gfa` files). Is there a way to obtain the phase sets/phasing blocks used in construction of these...
Hi again, Apologies for opening a new issue but this time it is on a different topic. We are trying to assemble a giant genome of ~30 Gb using 70x...
How effective is hifiasm in assembling continuous regions with uneven coverage? Moreover, how effective is hifiasm when inputting regions that are discontinuous and have uneven coverage?
Hi, I am trying to assemble a phased genome of a hexaploid species (expected genome size ~ 4Gb) with 356 GB HiFi reads and 85 GB omni C data. However,...
Hi, I have a 0.9Gbp plant genome with HiFi and Hi-C data. HiFiasm has given me an assembly the correct size with 1000 contigs. Can you please clarify this paragraph...
Usually, we convert hifiasm gfa file using awk like this: `awk '/^S/{print ">"$2;print $3}' test.p_ctg.gfa > test.p_ctg.fa` [(Ref)](https://hifiasm.readthedocs.io/en/latest/faq.html#how-do-i-get-contigs-in-fasta) Why do we ignore contig's links (Lines started with "L" containing links...
Hi, I utilized HiFiasm to assemble an insect genome solely using HiFi reads. I systematically experimented with different -s values, namely 0.75, 0.55, 0.50, 0.45, 0.3, 0.2, and 0.1. Surprisingly,...
In the review article "Genome assembly in the telomere-to-telomere era", @lh3 and @richarddurbin have mentioned that: > When constructing an overlap graph, we discard a read contained in longer reads....
