2024 Github hifiasm

Github hifiasm

Author: ywgj

August undefined, 2024

WebHello, When I performed hic scaffolding of the hifiasm contigs, as we can see from the picture, the end of the group 12a contig contains two times alletic segments (which should be cut and assign one part to group 12b) , but this is an entire contig from hifiasm. WebThanks for letting us know. This is a specific issue for 0.18.5-r499.We are trying to fix it as soon as possible. Could you please use Hifiasm-0.18.4-r496 beta or Hifiasm-0.18.2-r467 beta first? Rerun 0.18.4 or 0.18.2 could reuse existing bin …

Aborted run · Issue #394 · chhylp123/hifiasm · GitHub

WebOct 25, 2024 · Shane, you are definitely right that hifiasm misinterpreted this k-mer histogram. I have implemented a fix at the "fix-49" branch. Could you have a look to see if it really fixes the issue? Thanks! PS: the fix skips the lower end of the k-mer spectrum when hifiasm attempts to look for the homozygous peak. The default is set to 5. WebYes, most modules of hifiasm are designed for diploid samples, including purge duplication step, partially phased assembly and fully-phased assembly with trio-binning or Hi-C. Are polyploid genomes supported? The *r_utg.gfa and *p_utg.gfa are lossless so that they also work for polyploid genomes. flax seed pics

Joining small contigs to large contigs #127 - GitHub

WebApr 11, 2024 · chhylp123 / hifiasm Public. Notifications Fork 61; Star 344. Code; Issues 212; Pull requests 4; Actions; Projects 0; Security; Insights ... Already on GitHub? Sign in to your account Jump to bottom [M::ha_opt_update_cov] updated max_n_chain to 910 #442. Open xfcypeng opened this issue Apr 11, 2024 · 1 comment Webuc_block_qse_cutoff assertion fail · Issue #441 · chhylp123/hifiasm · GitHub. chhylp123. Notifications. Fork 61. Star 341. Projects. Insights. WebAug 7, 2024 · Contribute to shilpagarg/pstools development by creating an account on GitHub. Use Hi-C data and node sequences of hifiasm graph (awk '/^S/{print ">"$2;print $3}' hifiasm_r_utg.gfa > hifiasm_r_utg.fa) pstools hic_mapping -t32 -o < map.out > < hifiasm_r_utg.fa > < hic.R1.fastq.gz > < hic.R2.fastq.gz > # Use Hi-C mapped reads … cheeseballs band

[M::ha_opt_update_cov] updated max_n_chain to 910 #442 - github.com

Hifiasm — hifiasm 0.16.0 documentation

WebHifiasm applies -a rounds of short overlap removal with an increasing threshold between FLOAT1 and FLOAT2. -i Ignore all bin files so that hifiasm will start again from scratch. -u Disable post-join step for contigs which may improve N50. The post-join step of hifiasm improves contig N50 but may introduce misassemblies. --hom-cov WebUsing #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead. To run Hifiasm on our clusters: … flaxseed pillows by franWebSep 24, 2024 · get a primary assembly by hifiasm partition corrected HiFi reads generated by hifiasm with HiC and hifiasm's primary assembly feed the read partition lists to hifiasm with the options '-3/-4'. This step will reuse the bin files generated by step 1. So it just does graph cleaning and does not perform reassembly. flaxseed phytoestrogen

"WebApr 20, 2024 · At first, my run command: hifiasm -z 50 -o THS.asm -t 20 ../1_data/THS_pacbio.fasta and ran for a week without any files output. I'm running commands on another server：hifiasm -z 50 -o THS.asm -t 60 THS_pacbio.fasta , I tried different threads parameters including 10，30, 100, and run for about a few hours and … " - Github hifiasm

Github hifiasm

fixing the mis-connection · Issue #440 · chhylp123/hifiasm · GitHub

WebDifferent Hifiasm versions yield large differences in haplotype assembly sizes · Issue #443 · chhylp123/hifiasm · GitHub chhylp123 / hifiasm Public Notifications Fork 61 Star 344 … WebMar 24, 2024 · S5 Table: Annotations and sequence similarities for genes within the inverted region on LG9 of B.pfeifferi genome in comparison to B.glabrata iM line. Multiple sheets in the Excel table recorded the details of the inversion between the two genomes: provided are inversion region locations; annotations and sequence similarities of 24 reciprocal best …

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WebAug 10, 2024 · Hi, @chhylp123 hifiasm works great on all my plant genome assembly, it produce more contiguous and complete genome in less resource usage.. But I recently assembly a fish genome with hifiasm, it have low contig N50.. Here is the all the information I have. Do you have any suggestions for tuning? genomscope estimation from the survey … WebMay 27, 2024 · The command mentioned is from hifiasm. What do you mean by: "can place contigs in chromosomal context, identify contaminant contigs, any missed duplicated haplotypes in primary assembly that could be purged, and validate the existing contigs for accuracy". BUSCO analysis with eudicots of my assmbled genome showed - 99.1%.

WebHifiasm dev debug CI #80: Pull request #420 opened by chhylp123. hifiasm_dev_debug. last month 3m 12s. Merge pull request #419 from chhylp123/hifiasm_dev_debug CI #79: Commit fa663a9 pushed by chhylp123. master. last month 2m 41s. Hifiasm dev debug CI #78: Pull request #419 opened by chhylp123. WebHi, Is there a parameter to output fully corrected or almost fully corrected UL reads in fasta or fastq format? Cheers,

WebSep 7, 2024 · chhylp123 / hifiasm Public Notifications Fork 60 Star 338 Code Issues 206 Pull requests 4 Actions Projects Security Insights New issue ERROR: this implementation supports no more than 268435456 reads #182 Closed iamnotaNL opened this issue on Sep 7, 2024 · 10 comments iamnotaNL commented on Sep 7, 2024 WebApr 13, 2024 · 嗨嗨嗨，你好！这是你第一次使用 HIFI数据进行基因组组装，如果你想学习如何使用canu和hifiasm对基因组进行初步组装, 可以仔细阅读这篇文章，了解一下这两 …

WebApr 17, 2024 · misassembly introduced in hifiasm v0.5 · Issue #10 · chhylp123/hifiasm · GitHub chhylp123 / hifiasm Public Notifications Fork 61 Star 341 Code Issues 211 Pull requests 4 Actions Projects Security Insights New issue misassembly introduced in hifiasm v0.5 #10 Closed HenrivdGeest opened this issue on Apr 17, 2024 · 16 comments

WebApr 13, 2024 · 嗨嗨嗨，你好！这是你第一次使用 HIFI数据进行基因组组装，如果你想学习如何使用canu和hifiasm对基因组进行初步组装, 可以仔细阅读这篇文章，了解一下这两个软件的基本使用方法。软件安装. 软件安装我推荐使用conda安装，配置好源之后方便快捷。当然要是对版本有要求可以选择自己编译安装 ... flaxseed pills side effectsWebHifiasm produces arguably the best single-sample telomere-to-telomere assemblies combing HiFi, ultralong and Hi-C reads, and it is one of the best haplotype-resolved … Issues 151 - GitHub - chhylp123/hifiasm: Hifiasm: a haplotype-resolved … Pull requests 3 - GitHub - chhylp123/hifiasm: Hifiasm: a haplotype … Actions - GitHub - chhylp123/hifiasm: Hifiasm: a haplotype-resolved … GitHub is where people build software. More than 83 million people use GitHub … GitHub is where people build software. More than 100 million people use … We would like to show you a description here but the site won’t allow us. Since Hifiasm-0.18.7 (r513): Hifiasm has a more accurate alignment procedure for … cheese ball serverWebHifiasm is a fast haplotype-resolved de novo assembler for PacBio HiFi reads. It can assemble a human genome in several hours and assemble a ~30Gb California redwood genome in a few days. Hifiasm emits partially phased assemblies of quality competitive with the best assemblers. flaxseed pills in smoothiesWebJan 27, 2024 · segmentation fault · Issue #69 · chhylp123/hifiasm · GitHub chhylp123 / hifiasm Public Notifications Fork 61 Star 342 Code Issues 212 Pull requests 4 Actions Projects Security Insights New issue segmentation fault #69 Closed Mrbland opened this issue on Jan 27, 2024 · 7 comments Mrbland commented on Jan 27, 2024 Hello, cheese balls calorie countWebNov 1, 2024 · · Issue #335 · chhylp123/hifiasm · GitHub chhylp123 / hifiasm Notifications Fork Star core dump when assembly a genome. #335 Open weifei007 opened this issue on Nov 1, 2024 · 1 comment weifei007 on Nov 1, 2024 Sign up for free to join this conversation on GitHub . Already have an account? Sign in to comment cheese balls barrel largeWebUsing #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead. To run Hifiasm on our clusters: #!/bin/bash #SBATCH -A myallocation # Allocation name #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=hifiasm #SBATCH --mail … flaxseed pills reviewsWebDec 22, 2024 · Just put multiple files on the command line. For typical HiFi data, no need to use -z.Like seqtk, minimap2, bwa, ... hifiasm seamlessly works with fasta, fastq and their gzip'd versions. cheese balls and logs