{"id":13704241,"url":"https://github.com/chhylp123/hifiasm","last_synced_at":"2025-05-05T09:33:31.032Z","repository":{"id":41269817,"uuid":"185860172","full_name":"chhylp123/hifiasm","owner":"chhylp123","description":"Hifiasm: a haplotype-resolved assembler for accurate Hifi reads ","archived":false,"fork":false,"pushed_at":"2024-10-17T05:34:07.000Z","size":14669,"stargazers_count":533,"open_issues_count":419,"forks_count":87,"subscribers_count":28,"default_branch":"master","last_synced_at":"2024-10-19T07:50:59.646Z","etag":null,"topics":["bioinformatics","denovo-assembly","genomics","hifi-read","pacbio"],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/chhylp123.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":"code_of_conduct.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-05-09T19:34:58.000Z","updated_at":"2024-10-17T09:34:08.000Z","dependencies_parsed_at":"2023-11-06T06:23:53.729Z","dependency_job_id":"711a72d4-21e2-4062-9920-592203a5c40b","html_url":"https://github.com/chhylp123/hifiasm","commit_stats":null,"previous_names":[],"tags_count":49,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chhylp123%2Fhifiasm","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chhylp123%2Fhifiasm/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chhylp123%2Fhifiasm/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chhylp123%2Fhifiasm/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/chhylp123","download_url":"https://codeload.github.com/chhylp123/hifiasm/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224439833,"owners_count":17311534,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","denovo-assembly","genomics","hifi-read","pacbio"],"created_at":"2024-08-02T21:01:06.174Z","updated_at":"2025-05-05T09:33:31.007Z","avatar_url":"https://github.com/chhylp123.png","language":"C++","funding_links":[],"categories":["Long-read sequencing","Ranked by starred repositories"],"sub_categories":["Long-read Assembly"],"readme":"## \u003ca name=\"started\"\u003e\u003c/a\u003eGetting Started\n\n```sh\n# Install hifiasm (requiring g++ and zlib)\ngit clone https://github.com/chhylp123/hifiasm\ncd hifiasm \u0026\u0026 make\n\n# Run on test data (use -f0 for small datasets)\nwget https://github.com/chhylp123/hifiasm/releases/download/v0.7/chr11-2M.fa.gz\n./hifiasm -o test -t4 -f0 chr11-2M.fa.gz 2\u003e test.log\nawk '/^S/{print \"\u003e\"$2;print $3}' test.bp.p_ctg.gfa \u003e test.p_ctg.fa  # get primary contigs in FASTA\n\n# Assemble inbred/homozygous genomes (-l0 disables duplication purging)\nhifiasm -o CHM13.asm -t32 -l0 CHM13-HiFi.fa.gz 2\u003e CHM13.asm.log\n# Assemble heterozygous genomes with built-in duplication purging\nhifiasm -o HG002.asm -t32 HG002-file1.fq.gz HG002-file2.fq.gz\n\n# Assemble genomes with ONT R10 reads rather than PacBio HiFi reads using the latest release of hifiasm (\u003e0.21.0-r686)\nhifiasm -o HG002.asm --ont -t32 HG002-ont.fq.gz\n\n# Hi-C phasing with paired-end short reads in two FASTQ files\nhifiasm -o HG002.asm --h1 read1.fq.gz --h2 read2.fq.gz HG002-HiFi.fq.gz\n\n# Trio binning assembly (requiring https://github.com/lh3/yak)\nyak count -b37 -t16 -o pat.yak \u003c(cat pat_1.fq.gz pat_2.fq.gz) \u003c(cat pat_1.fq.gz pat_2.fq.gz)\nyak count -b37 -t16 -o mat.yak \u003c(cat mat_1.fq.gz mat_2.fq.gz) \u003c(cat mat_1.fq.gz mat_2.fq.gz)\nhifiasm -o HG002.asm -t32 -1 pat.yak -2 mat.yak HG002-HiFi.fa.gz\n\n# Improve contiguity for diploid genome assembly by self-scaffolding (`--dual-scaf`)\nhifiasm -o HG002.asm --dual-scaf --h1 read1.fq.gz --h2 read2.fq.gz HG002-HiFi.fq.gz\n\n# Preserve more telomeres for human genomes (`--telo-m CCCTAA`)\nhifiasm -o HG002.asm --telo-m CCCTAA --h1 read1.fq.gz --h2 read2.fq.gz HG002-HiFi.fq.gz\n\n# Hybrid assembly with HiFi, ultralong and Hi-C reads\nhifiasm -o HG002.asm --h1 read1.fq.gz --h2 read2.fq.gz --ul ul.fq.gz HG002-HiFi.fq.gz\n\n# Single-sample telomere-to-telomere assembly for diploid human genomes\nhifiasm -o HG002.asm --dual-scaf --telo-m CCCTAA --h1 read1.fq.gz --h2 read2.fq.gz --ul ul.fq.gz HG002-HiFi.fq.gz\n\n```\nSee [tutorial][tutorial] for more details. \n\n## Table of Contents\n\n- [Getting Started](#started)\n- [Introduction](#intro)\n- [Why Hifiasm?](#why)\n- [Usage](#use)\n  - [Assembling HiFi reads without additional data types](#hifionly)\n  - [Assembling ONT reads](#ontonly)\n  - [Hi-C integration](#hic)\n  - [Trio binning](#trio)\n  - [Ultra-long ONT integration](#ul)\n  - [Output files](#output)\n- [Results](#results)\n- [Getting Help](#help)\n- [Limitations](#limit)\n- [Citing Hifiasm](#cite)\n\n## \u003ca name=\"intro\"\u003e\u003c/a\u003eIntroduction\n\nHifiasm is a fast haplotype-resolved de novo assembler initially designed for PacBio HiFi reads.\nIts latest release could support the telomere-to-telomere assembly by utilizing ultralong Oxford Nanopore reads. Hifiasm 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 assemblers for the trio-binning assembly given parental short reads. For a human genome, hifiasm can produce the telomere-to-telomere assembly in one day.\n\n## \u003ca name=\"why\"\u003e\u003c/a\u003eWhy Hifiasm?\n\n* Hifiasm delivers high-quality telomere-to-telomere assemblies. It tends to generate longer contigs\n  and resolve more segmental duplications than other assemblers.\n\n* Given Hi-C reads or short reads from the parents, hifiasm can produce overall the best\n  haplotype-resolved assembly so far. It is the assembler of choice by the\n  [Human Pangenome Project][hpp] for the first batch of samples.\n\n* Hifiasm can purge duplications between haplotigs without relying on\n  third-party tools such as purge\\_dups. Hifiasm does not need polishing tools\n  like pilon or racon, either. This simplifies the assembly pipeline and saves\n  running time.\n\n* Hifiasm is fast. It can assemble a human genome in half a day and assemble a\n  ~30Gb redwood genome in three days. No genome is too large for hifiasm.\n\n* Hifiasm is trivial to install and easy to use. It does not required Python,\n  R or C++11 compilers, and can be compiled into a single executable. The\n  default setting works well with a variety of genomes.\n\n[hpp]: https://humanpangenome.org\n\n## \u003ca name=\"use\"\u003e\u003c/a\u003eUsage\n\n### \u003ca name=\"hifionly\"\u003e\u003c/a\u003eAssembling HiFi reads without additional data types\n\nA typical hifiasm command line looks like:\n```sh\nhifiasm -o NA12878.asm -t 32 NA12878.fq.gz\n```\nwhere `NA12878.fq.gz` provides the input reads, `-t` sets the number of CPUs in\nuse and `-o` specifies the prefix of output files. For this example, the\nprimary contigs are written to `NA12878.asm.bp.p_ctg.gfa`. \nSince v0.15, hifiasm also produces two sets of\npartially phased contigs at `NA12878.asm.bp.hap?.p_ctg.gfa`. This pair of files\ncan be thought to represent the two haplotypes in a diploid genome, though with\noccasional switch errors. The frequency of switches is determined by the\nheterozygosity of the input sample.\n\nAt the first run, hifiasm saves corrected reads and\noverlaps to disk as `NA12878.asm.*.bin`. It reuses the saved results to avoid\nthe time-consuming all-vs-all overlap calculation next time. You may specify\n`-i` to ignore precomputed overlaps and redo overlapping from raw reads.\nYou can also dump error corrected reads in FASTA and read overlaps in PAF with\n```sh\nhifiasm -o NA12878.asm -t 32 --write-paf --write-ec /dev/null\n```\n\nHifiasm purges haplotig duplications by default. For inbred or homozygous\ngenomes, you may disable purging with option `-l0`. Old HiFi reads may contain\nshort adapter sequences at the ends of reads. You can specify `-z20` to trim\nboth ends of reads by 20bp. For small genomes, use `-f0` to disable the initial\nbloom filter which takes 16GB memory at the beginning. For genomes much larger\nthan human, applying `-f38` or even `-f39` is preferred to save memory on k-mer\ncounting.\n\n### \u003ca name=\"ontonly\"\u003e\u003c/a\u003eAssembling ONT reads\n\nSince version 0.21.0 (r686), hifiasm can support ONT assembly using ONT simplex R10 reads. \nTo enable this feature, add the `--ont` option as shown below:\n```sh\nhifiasm -t64 --ont -o ONT.asm ONT.read.fastq.gz\n```\nPlease note that this module requires input reads in FASTQ format.\n\n\n### \u003ca name=\"hic\"\u003e\u003c/a\u003eHi-C integration\n\nHifiasm can generate a pair of haplotype-resolved assemblies with paired-end\nHi-C reads:\n```sh\nhifiasm -o NA12878.asm -t32 --h1 read1.fq.gz --h2 read2.fq.gz HiFi-reads.fq.gz\n```\nIn this mode, each contig is supposed to be a haplotig, which by definition\ncomes from one parental haplotype only. Hifiasm often puts all contigs from the\nsame parental chromosome in one assembly. It has cleanly separated chrX and\nchrY for a human male dataset. Nonetheless, phasing across centromeres is\nchallenging. Hifiasm is often able to phase entire chromosomes but it may fail \nin rare cases. Also, contigs from different parental chromosomes are randomly mixed as\nit is just not possible to phase across chromosomes with Hi-C.\n\nHifiasm does not perform scaffolding for now. You need to run a standalone\nscaffolder such as SALSA or 3D-DNA to scaffold phased haplotigs.\n\n### \u003ca name=\"trio\"\u003e\u003c/a\u003eTrio binning\n\nWhen parental short reads are available, hifiasm can also generate a pair of\nhaplotype-resolved assemblies with trio binning. To perform such assembly, you\nneed to count k-mers first with [yak][yak] first and then do assembly:\n```sh\nyak count -k31 -b37 -t16 -o pat.yak paternal.fq.gz\nyak count -k31 -b37 -t16 -o mat.yak maternal.fq.gz\nhifiasm -o NA12878.asm -t 32 -1 pat.yak -2 mat.yak NA12878.fq.gz\n```\nHere `NA12878.asm.dip.hap1.p_ctg.gfa` and `NA12878.asm.dip.hap2.p_ctg.gfa` give the two\nhaplotype assemblies. In the binning mode, hifiasm does not purge haplotig\nduplicates by default. Because hifiasm reuses saved overlaps, you can\ngenerate both primary/alternate assemblies and trio binning assemblies with\n```sh\nhifiasm -o NA12878.asm -t 32 NA12878.fq.gz 2\u003e NA12878.asm.pri.log\nhifiasm -o NA12878.asm -t 32 -1 pat.yak -2 mat.yak /dev/null 2\u003e NA12878.asm.trio.log\n```\nThe second command line will run much faster than the first.\n\n### \u003ca name=\"ul\"\u003e\u003c/a\u003eUltra-long ONT integration\n\nHifiasm could integrate ultra-long ONT reads to produce the telomere-to-telomere assembly:\n```sh\nhifiasm -o NA12878.asm -t32 --ul ul.fq.gz HiFi-reads.fq.gz\n```\nFor the single-sample telomere-to-telomere assembly with Hi-C reads:\n```sh\nhifiasm -o NA12878.asm -t32 --ul ul.fq.gz --h1 read1.fq.gz --h2 read2.fq.gz HiFi-reads.fq.gz\n```\nFor the trio-binning telomere-to-telomere assembly:\n```sh\nhifiasm -o NA12878.asm -t32 --ul ul.fq.gz -1 pat.yak -2 mat.yak HiFi-reads.fq.gz\n```\n\n### \u003ca name=\"ul\"\u003e\u003c/a\u003eSelf-scaffolding\n\nFor diploid haplotype-resolved genome assembly, hifiasm can further enhance assembly contiguity \nby introducing scaffolding. It leverages the assemblies of the two haplotypes to scaffold each other. \nSpecifically, if there is a gap within the haplotype 1 assembly, hifiasm will use the corresponding \nhomologous region in haplotype 2 to scaffold haplotype 1. Below is an example using the `--dual-scaf` option.\n```sh\nhifiasm -o NA12878.asm -t32 --dual-scaf HiFi-reads.fq.gz\n```\n\n### \u003ca name=\"ul\"\u003e\u003c/a\u003ePreserve more telomeres for T2T assemblies\n\nHifiasm can preserve more telomeres by specifying the telomere motif using the `--telo-m` option. \nBelow is an example applied to human genome assembly.\n```sh\nhifiasm -o NA12878.asm -t32 --telo-m CCCTAA HiFi-reads.fq.gz\n```\n\n### \u003ca name=\"output\"\u003e\u003c/a\u003eOutput files\n\nHifiasm generates different types of assemblies based on the input data. \nIt also writes error corrected reads to the *prefix*.ec.bin binary file and\nwrites overlaps to *prefix*.ovlp.source.bin and *prefix*.ovlp.reverse.bin.\nFor more details, please see the complete [documentation][tutorial_output].\n\n## \u003ca name=\"results\"\u003e\u003c/a\u003eResults\n\nThe following table shows the statistics of several hifiasm primary assemblies assembled with v0.12:\n\n|\u003csub\u003eDataset\u003csub\u003e|\u003csub\u003eSize\u003csub\u003e|\u003csub\u003eCov.\u003csub\u003e|\u003csub\u003eAsm options\u003csub\u003e|\u003csub\u003eCPU time\u003csub\u003e|\u003csub\u003eWall time\u003csub\u003e|\u003csub\u003eRAM\u003csub\u003e|\u003csub\u003e N50\u003csub\u003e|\n|:---------------|-----:|-----:|:---------------------|-------:|--------:|----:|----------------:|\n|\u003csub\u003e[Mouse (C57/BL6J)][mouse-data]\u003c/sub\u003e|\u003csub\u003e2.6Gb\u003c/sub\u003e |\u003csub\u003e\u0026times;25\u003c/sub\u003e|\u003csub\u003e-t48 -l0\u003c/sub\u003e |\u003csub\u003e172.9h\u003c/sub\u003e |\u003csub\u003e4.8h\u003c/sub\u003e |\u003csub\u003e76G\u003c/sub\u003e |\u003csub\u003e21.1Mb\u003c/sub\u003e|\n|\u003csub\u003e[Maize (B73)][maize-data]\u003c/sub\u003e     |\u003csub\u003e2.2Gb\u003c/sub\u003e |\u003csub\u003e\u0026times;22\u003c/sub\u003e|\u003csub\u003e-t48 -l0\u003c/sub\u003e |\u003csub\u003e203.2h\u003c/sub\u003e |\u003csub\u003e5.1h\u003c/sub\u003e |\u003csub\u003e68G\u003c/sub\u003e |\u003csub\u003e36.7Mb\u003c/sub\u003e|\n|\u003csub\u003e[Strawberry][strawberry-data]\u003c/sub\u003e |\u003csub\u003e0.8Gb\u003c/sub\u003e |\u003csub\u003e\u0026times;36\u003c/sub\u003e|\u003csub\u003e-t48 -D10\u003c/sub\u003e|\u003csub\u003e152.7h\u003c/sub\u003e |\u003csub\u003e3.7h\u003c/sub\u003e |\u003csub\u003e91G\u003c/sub\u003e |\u003csub\u003e17.8Mb\u003c/sub\u003e|\n|\u003csub\u003e[Frog][frog-data]\u003c/sub\u003e             |\u003csub\u003e9.5Gb\u003c/sub\u003e |\u003csub\u003e\u0026times;29\u003c/sub\u003e|\u003csub\u003e-t48\u003c/sub\u003e     |\u003csub\u003e2834.3h\u003c/sub\u003e|\u003csub\u003e69.0h\u003c/sub\u003e|\u003csub\u003e463G\u003c/sub\u003e|\u003csub\u003e9.3Mb\u003c/sub\u003e|\n|\u003csub\u003e[Redwood][redwood-data]\u003c/sub\u003e       |\u003csub\u003e35.6Gb\u003c/sub\u003e|\u003csub\u003e\u0026times;28\u003c/sub\u003e|\u003csub\u003e-t80\u003c/sub\u003e     |\u003csub\u003e3890.3h\u003c/sub\u003e|\u003csub\u003e65.5h\u003c/sub\u003e|\u003csub\u003e699G\u003c/sub\u003e|\u003csub\u003e5.4Mb\u003c/sub\u003e|\n|\u003csub\u003e[Human (CHM13)][CHM13-data]\u003c/sub\u003e   |\u003csub\u003e3.1Gb\u003c/sub\u003e |\u003csub\u003e\u0026times;32\u003c/sub\u003e|\u003csub\u003e-t48 -l0\u003c/sub\u003e |\u003csub\u003e310.7h\u003c/sub\u003e |\u003csub\u003e8.2h\u003c/sub\u003e |\u003csub\u003e114G\u003c/sub\u003e|\u003csub\u003e88.9Mb\u003c/sub\u003e|\n|\u003csub\u003e[Human (HG00733)][HG00733-data]\u003c/sub\u003e|\u003csub\u003e3.1Gb\u003c/sub\u003e|\u003csub\u003e\u0026times;33\u003c/sub\u003e|\u003csub\u003e-t48\u003c/sub\u003e     |\u003csub\u003e269.1h\u003c/sub\u003e |\u003csub\u003e6.9h\u003c/sub\u003e |\u003csub\u003e135G\u003c/sub\u003e|\u003csub\u003e69.9Mb\u003c/sub\u003e|\n|\u003csub\u003e[Human (HG002)][NA24385-data]\u003c/sub\u003e |\u003csub\u003e3.1Gb\u003c/sub\u003e |\u003csub\u003e\u0026times;36\u003c/sub\u003e|\u003csub\u003e-t48\u003c/sub\u003e     |\u003csub\u003e305.4h\u003c/sub\u003e |\u003csub\u003e7.7h\u003c/sub\u003e |\u003csub\u003e137G\u003c/sub\u003e|\u003csub\u003e98.7Mb\u003c/sub\u003e|\n\n[mouse-data]:      https://www.ncbi.nlm.nih.gov/sra/?term=SRR11606870\n[maize-data]:      https://www.ncbi.nlm.nih.gov/sra/?term=SRR11606869\n[strawberry-data]: https://www.ncbi.nlm.nih.gov/sra/?term=SRR11606867\n[frog-data]:       https://www.ncbi.nlm.nih.gov/sra?term=(SRR11606868)%20OR%20SRR12048570\n[redwood-data]:    https://www.ncbi.nlm.nih.gov/sra/?term=SRP251156\n[CHM13-data]:      https://www.ncbi.nlm.nih.gov/sra?term=(((SRR11292120)%20OR%20SRR11292121)%20OR%20SRR11292122)%20OR%20SRR11292123\n\nHifiasm can assemble a 3.1Gb human genome in several hours or a ~30Gb hexaploid\nredwood genome in a few days on a single machine. For trio binning assembly:\n\n|\u003csub\u003eDataset\u003csub\u003e|\u003csub\u003eCov.\u003csub\u003e|\u003csub\u003eCPU time\u003csub\u003e|\u003csub\u003eElapsed time\u003csub\u003e|\u003csub\u003eRAM\u003csub\u003e|\u003csub\u003e N50\u003csub\u003e|\n|:---------------|-----:|-------:|--------:|----:|----------------:|\n|\u003csub\u003e[HG00733][HG00733-data], [\\[father\\]][HG00731-data], [\\[mother\\]][HG00732-data]\u003c/sub\u003e|\u003csub\u003e\u0026times;33\u003c/sub\u003e|\u003csub\u003e269.1h\u003c/sub\u003e|\u003csub\u003e6.9h\u003c/sub\u003e|\u003csub\u003e135G\u003c/sub\u003e|\u003csub\u003e35.1Mb (paternal), 34.9Mb (maternal)\u003c/sub\u003e|\n|\u003csub\u003e[HG002][NA24385-data],   [\\[father\\]][NA24149-data], [\\[mother\\]][NA24143-data]\u003c/sup\u003e|\u003csub\u003e\u0026times;36\u003c/sub\u003e|\u003csub\u003e305.4h\u003c/sub\u003e|\u003csub\u003e7.7h\u003c/sub\u003e|\u003csub\u003e137G\u003c/sub\u003e|\u003csub\u003e41.0Mb (paternal), 40.8Mb (maternal)\u003c/sub\u003e|\n\n\u003c!--\n|\u003csub\u003e[NA12878][NA12878-data], [\\[father\\]][NA12891-data], [\\[mother\\]][NA12892-data]\u003c/sub\u003e|\u003csub\u003e\u0026times;30\u003c/sub\u003e|\u003csub\u003e180.8h\u003c/sub\u003e|\u003csub\u003e4.9h\u003c/sub\u003e|\u003csub\u003e123G\u003c/sub\u003e|\u003csub\u003e27.7Mb (paternal), 27.0Mb (maternal)\u003c/sub\u003e|\n--\u003e\n\n[HG00733-data]: https://www.ebi.ac.uk/ena/data/view/ERX3831682\n[HG00731-data]: https://www.ebi.ac.uk/ena/data/view/ERR3241754\n[HG00732-data]: https://www.ebi.ac.uk/ena/data/view/ERR3241755\n[NA24385-data]: https://www.ncbi.nlm.nih.gov/sra?term=(((SRR10382244)%20OR%20SRR10382245)%20OR%20SRR10382248)%20OR%20SRR10382249\n[NA24149-data]: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG003_NA24149_father/NIST_HiSeq_HG003_Homogeneity-12389378/HG003Run01-13262252/\n[NA24143-data]: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG004_NA24143_mother/NIST_HiSeq_HG004_Homogeneity-14572558/HG004Run01-15133132/\n[NA12878-data]: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/PacBio_SequelII_CCS_11kb/\n[NA12891-data]: https://www.ebi.ac.uk/ena/data/view/ERR194160\n[NA12892-data]: https://www.ebi.ac.uk/ena/data/view/ERR194161\n\nHuman assemblies above can be acquired [from Zenodo][zenodo-human] and\nnon-human ones are available [here][zenodo-nonh].\n\n[zenodo-human]: https://zenodo.org/record/4393631\n[zenodo-nonh]: https://zenodo.org/record/4393750\n[unitig]: http://wgs-assembler.sourceforge.net/wiki/index.php/Celera_Assembler_Terminology\n[gfa]: https://github.com/pmelsted/GFA-spec/blob/master/GFA-spec.md\n[paf]: https://github.com/lh3/miniasm/blob/master/PAF.md\n[yak]: https://github.com/lh3/yak\n[tutorial]: https://hifiasm.readthedocs.io/en/latest/index.html\n[tutorial_output]: https://hifiasm.readthedocs.io/en/latest/interpreting-output.html#interpreting-output\n\n\n## \u003ca name=\"help\"\u003e\u003c/a\u003eGetting Help\n\nFor detailed description of options, please see [tutorial][tutorial] or `man ./hifiasm.1`. The `-h`\noption of hifiasm also provides brief description of options. If you have\nfurther questions, please raise an issue at the [issue\npage](https://github.com/chhylp123/hifiasm/issues).\n\n## \u003ca name=\"limit\"\u003e\u003c/a\u003eLimitations\n\n1. Purging haplotig duplications may introduce misassemblies.\n\n## \u003ca name=\"cite\"\u003e\u003c/a\u003eCitating Hifiasm\n\nIf you use hifiasm in your work, please cite:\n\n\u003e Cheng, H., Concepcion, G.T., Feng, X., Zhang, H., Li H. (2021)\n\u003e Haplotype-resolved de novo assembly using phased assembly graphs with\n\u003e hifiasm. *Nat Methods*, **18**:170-175.\n\u003e https://doi.org/10.1038/s41592-020-01056-5\n\n\u003e Cheng, H., Jarvis, E.D., Fedrigo, O., Koepfli, K.P., Urban, L., Gemmell, N.J., Li, H. (2022)\n\u003e Haplotype-resolved assembly of diploid genomes without parental data. \n\u003e *Nature Biotechnology*, **40**:1332–1335.\n\u003e https://doi.org/10.1038/s41587-022-01261-x\n\n\u003e Cheng, H., Asri, M., Lucas, J., Koren, S., Li, H. (2024)\n\u003e Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. \n\u003e *Nat Methods*, **21**:967-970.\n\u003e https://doi.org/10.1038/s41592-024-02269-8\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchhylp123%2Fhifiasm","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fchhylp123%2Fhifiasm","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchhylp123%2Fhifiasm/lists"}