{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T16:15:12Z","timestamp":1787242512741,"version":"3.56.0"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2023,10,5]],"date-time":"2023-10-05T00:00:00Z","timestamp":1696464000000},"content-version":"vor","delay-in-days":13,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["16H06279"],"award-info":[{"award-number":["16H06279"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["15H05606"],"award-info":[{"award-number":["15H05606"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["19H03274"],"award-info":[{"award-number":["19H03274"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["20H03305"],"award-info":[{"award-number":["20H03305"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["17H03723"],"award-info":[{"award-number":["17H03723"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Although current long-read sequencing technologies have a long-read length that facilitates assembly for genome reconstruction, they have high sequence errors. While various assemblers with different perspectives have been developed, no systematic evaluation of assemblers with long reads for diploid genomes with varying heterozygosity has been performed. Here, we evaluated a series of processes, including the estimation of genome characteristics such as genome size and heterozygosity, de novo assembly, polishing, and removal of allelic contigs, using six genomes with various heterozygosity levels. We evaluated five long-read-only assemblers (Canu, Flye, miniasm, NextDenovo and Redbean) and five hybrid assemblers that combine short and long reads (HASLR, MaSuRCA, Platanus-allee, SPAdes and WENGAN) and proposed a concrete guideline for the construction of haplotype representation according to the degree of heterozygosity, followed by polishing and purging haplotigs, using stable and high-performance assemblers: Redbean, Flye and MaSuRCA.<\/jats:p>","DOI":"10.1093\/bib\/bbad337","type":"journal-article","created":{"date-parts":[[2023,10,6]],"date-time":"2023-10-06T01:39:48Z","timestamp":1696556388000},"source":"Crossref","is-referenced-by-count":13,"title":["A practical assembly guideline for genomes with various levels of heterozygosity"],"prefix":"10.1093","volume":"24","author":[{"given":"Takako","family":"Mochizuki","sequence":"first","affiliation":[{"name":"Genome Informatics Laboratory, National Institute of Genetics"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mika","family":"Sakamoto","sequence":"additional","affiliation":[{"name":"Genome Informatics Laboratory, National Institute of Genetics"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasuhiro","family":"Tanizawa","sequence":"additional","affiliation":[{"name":"Genome Informatics Laboratory, National Institute of Genetics"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takuro","family":"Nakayama","sequence":"additional","affiliation":[{"name":"Division of Life Sciences Center for Computational Sciences, University of Tsukuba , Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Goro","family":"Tanifuji","sequence":"additional","affiliation":[{"name":"Department of Zoology, National Museum of Nature and Science"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryoma","family":"Kamikawa","sequence":"additional","affiliation":[{"name":"Graduate School of Agriculture, Kyoto University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasukazu","family":"Nakamura","sequence":"additional","affiliation":[{"name":"Genome Informatics Laboratory, National Institute of Genetics"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,10,5]]},"reference":[{"key":"2023100601374262400_ref1","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1038\/s41576-018-0003-4","article-title":"Piercing the dark matter: bioinformatics of long-range sequencing and mapping","volume":"19","author":"Sedlazeck","year":"2018","journal-title":"Nat Rev Genet"},{"key":"2023100601374262400_ref2","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s13059-020-1935-5","article-title":"Opportunities and challenges in long-read sequencing data analysis","volume":"21","author":"Amarasinghe","year":"2020","journal-title":"Genome Biol"},{"key":"2023100601374262400_ref3","doi-asserted-by":"crossref","first-page":"giab020","DOI":"10.1093\/gigascience\/giab020","article-title":"A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas","volume":"10","author":"Pe\u00f1aloza","year":"2021","journal-title":"GigaScience"},{"key":"2023100601374262400_ref4","doi-asserted-by":"crossref","first-page":"5817","DOI":"10.1038\/s41467-020-19682-0","article-title":"Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding","volume":"11","author":"Wang","year":"2020","journal-title":"Nat Commun"},{"key":"2023100601374262400_ref5","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1038\/nature22971","article-title":"Improved maize reference genome with single-molecule technologies","volume":"546","author":"Jiao","year":"2017","journal-title":"Nature"},{"key":"2023100601374262400_ref6","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1038\/nature21370","article-title":"The genome of Chenopodium quinoa","volume":"542","author":"Jarvis","year":"2017","journal-title":"Nature"},{"key":"2023100601374262400_ref7","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1038\/s41587-018-0004-z","article-title":"Errors in long-read assemblies can critically affect protein prediction","volume":"37","author":"Watson","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2023100601374262400_ref8","doi-asserted-by":"crossref","first-page":"giz160","DOI":"10.1093\/gigascience\/giz160","article-title":"The draft nuclear genome assembly of Eucalyptus pauciflora: a pipeline for comparing de novo assemblies","volume":"9","author":"Wang","year":"2020","journal-title":"GigaScience"},{"key":"2023100601374262400_ref9","doi-asserted-by":"crossref","first-page":"866","DOI":"10.1093\/bib\/bbx147","article-title":"Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data","volume":"20","author":"Jayakumar","year":"2019","journal-title":"Brief Bioinform"},{"key":"2023100601374262400_ref10","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1038\/s41467-020-14779-y","article-title":"Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics","volume":"11","author":"Jiao","year":"2020","journal-title":"Nat Commun"},{"key":"2023100601374262400_ref11","doi-asserted-by":"crossref","first-page":"1941","DOI":"10.1093\/bioinformatics\/btab048","article-title":"De novo genome assembly of Solanum sitiens reveals structural variation associated with drought and salinity tolerance","volume":"37","author":"Molitor","year":"2021","journal-title":"Bioinformatics"},{"key":"2023100601374262400_ref12","doi-asserted-by":"crossref","first-page":"4247","DOI":"10.1038\/s41467-021-24528-4","article-title":"The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts","volume":"12","author":"Wan","year":"2021","journal-title":"Nat Commun"},{"key":"2023100601374262400_ref13","doi-asserted-by":"crossref","first-page":"evab001","DOI":"10.1093\/gbe\/evab001","article-title":"Genomic evidence of an ancient east Asian divergence event in wild Saccharomyces cerevisiae","volume":"13","author":"Bendixsen","year":"2021","journal-title":"Genome Biol Evol"},{"key":"2023100601374262400_ref14","doi-asserted-by":"crossref","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"Walker","year":"2014","journal-title":"PloS One"},{"key":"2023100601374262400_ref15","doi-asserted-by":"crossref","first-page":"e1007981","DOI":"10.1371\/journal.pcbi.1007981","article-title":"The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies","volume":"16","author":"Zimin","year":"2020","journal-title":"PLoS Comput Biol"},{"key":"2023100601374262400_ref16","doi-asserted-by":"crossref","first-page":"2253","DOI":"10.1093\/bioinformatics\/btz891","article-title":"NextPolish: a fast and efficient genome polishing tool for long-read assembly","volume":"36","author":"Hu","year":"2020","journal-title":"Bioinformatics"},{"key":"2023100601374262400_ref17","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1038\/s41587-019-0217-9","article-title":"Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome","volume":"37","author":"Wenger","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2023100601374262400_ref18","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","article-title":"Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm","volume":"18","author":"Cheng","year":"2021","journal-title":"Nat Methods"},{"key":"2023100601374262400_ref19","doi-asserted-by":"crossref","first-page":"1291","DOI":"10.1101\/gr.263566.120","article-title":"HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads","volume":"30","author":"Nurk","year":"2020","journal-title":"Genome Res"},{"key":"2023100601374262400_ref20","first-page":"662","article-title":"De novo hybrid assembled draft genome of Commiphora wightii (Arnott) Bhandari reveals key enzymes involved in phytosterol biosynthesis","volume":"13","author":"Banerjee","year":"2023","journal-title":"Life (Basel)"},{"key":"2023100601374262400_ref21","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1186\/s12864-023-09286-5","article-title":"Division of developmental phases of freshwater leech Whitmania pigra and key genes related to neurogenesis revealed by whole genome and transcriptome analysis","volume":"24","author":"Liu","year":"2023","journal-title":"BMC Genomics"},{"key":"2023100601374262400_ref22","doi-asserted-by":"crossref","first-page":"1129319","DOI":"10.3389\/fmicb.2023.1129319","article-title":"Chromosome-level analysis of the Colletotrichum graminicola genome reveals the unique characteristics of core and minichromosomes","volume":"14","author":"Becerra","year":"2023","journal-title":"Front Microbiol"},{"key":"2023100601374262400_ref23","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation","volume":"27","author":"Koren","year":"2017","journal-title":"Genome Res"},{"key":"2023100601374262400_ref24","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2023100601374262400_ref25","doi-asserted-by":"crossref","first-page":"2103","DOI":"10.1093\/bioinformatics\/btw152","article-title":"Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences","volume":"32","author":"Li","year":"2016","journal-title":"Bioinformatics"},{"key":"2023100601374262400_ref26","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41592-019-0669-3","article-title":"Fast and accurate long-read assembly with wtdbg2","volume":"17","author":"Ruan","year":"2020","journal-title":"Nat Methods"},{"key":"2023100601374262400_ref27","doi-asserted-by":"crossref","first-page":"101389","DOI":"10.1016\/j.isci.2020.101389","article-title":"HASLR: fast hybrid assembly of long reads","volume":"23","author":"Haghshenas","year":"2020","journal-title":"iScience"},{"key":"2023100601374262400_ref28","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1101\/gr.213405.116","article-title":"Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm","volume":"27","author":"Zimin","year":"2017","journal-title":"Genome Res"},{"key":"2023100601374262400_ref29","doi-asserted-by":"crossref","first-page":"1702","DOI":"10.1038\/s41467-019-09575-2","article-title":"Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions","volume":"10","author":"Kajitani","year":"2019","journal-title":"Nat Commun"},{"key":"2023100601374262400_ref30","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1093\/bioinformatics\/btv688","article-title":"hybridSPAdes: an algorithm for hybrid assembly of short and long reads","volume":"32","author":"Antipov","year":"2016","journal-title":"Bioinformatics"},{"key":"2023100601374262400_ref31","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1038\/s41587-020-00747-w","article-title":"Efficient hybrid de novo assembly of human genomes with WENGAN","volume":"39","author":"Di Genova","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2023100601374262400_ref32","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1038\/nmeth.4035","article-title":"Phased diploid genome assembly with single-molecule real-time sequencing","volume":"13","author":"Chin","year":"2016","journal-title":"Nat Methods"},{"key":"2023100601374262400_ref33","doi-asserted-by":"crossref","first-page":"1384","DOI":"10.1101\/gr.170720.113","article-title":"Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads","volume":"24","author":"Kajitani","year":"2014","journal-title":"Genome Res"},{"key":"2023100601374262400_ref34","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1186\/s12859-018-2485-7","article-title":"Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies","volume":"19","author":"Roach","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"2023100601374262400_ref35","doi-asserted-by":"crossref","first-page":"2896","DOI":"10.1093\/bioinformatics\/btaa025","article-title":"Identifying and removing haplotypic duplication in primary genome assemblies","volume":"36","author":"Guan","year":"2020","journal-title":"Bioinformatics"},{"key":"2023100601374262400_ref36","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1093\/bioinformatics\/btx220","article-title":"HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly","volume":"33","author":"Huang","year":"2017","journal-title":"Bioinformatics"},{"key":"2023100601374262400_ref37","doi-asserted-by":"crossref","first-page":"eabi5075","DOI":"10.1126\/sciadv.abi5075","article-title":"Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida","volume":"8","author":"Kamikawa","year":"2022","journal-title":"Sci Adv"},{"key":"2023100601374262400_ref38","doi-asserted-by":"crossref","first-page":"e1005954","DOI":"10.1371\/journal.pgen.1005954","article-title":"Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding","volume":"12","author":"Vij","year":"2016","journal-title":"PLoS Genet"},{"key":"2023100601374262400_ref39","doi-asserted-by":"crossref","first-page":"D28","DOI":"10.1093\/nar\/gkq967","article-title":"The European nucleotide archive","volume":"39","author":"Leinonen","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023100601374262400_ref40","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1093\/bioinformatics\/btr011","article-title":"A fast, lock-free approach for efficient parallel counting of occurrences of k-mers","volume":"27","author":"Mar\u00e7ais","year":"2011","journal-title":"Bioinformatics"},{"key":"2023100601374262400_ref41","doi-asserted-by":"crossref","first-page":"2202","DOI":"10.1093\/bioinformatics\/btx153","article-title":"GenomeScope: fast reference-free genome profiling from short reads","volume":"33","author":"Vurture","year":"2017","journal-title":"Bioinformatics"},{"key":"2023100601374262400_ref42","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2023100601374262400_ref43","doi-asserted-by":"crossref","first-page":"e0163962","DOI":"10.1371\/journal.pone.0163962","article-title":"SeqKit: a cross-platform and ultrafast toolkit for FASTA\/Q file manipulation","volume":"11","author":"Shen","year":"2016","journal-title":"PloS One"},{"key":"2023100601374262400_ref44","first-page":"314","article-title":"Efficient architecture-aware acceleration of BWA-MEM for multicore systems","volume-title":"IEEE International Parallel and Distributed Processing Symposium (IPDPS)","author":"Vasimuddin","year":"2019"},{"key":"2023100601374262400_ref45","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023100601374262400_ref46","doi-asserted-by":"crossref","first-page":"2818","DOI":"10.1093\/bioinformatics\/btn548","article-title":"Aggressive assembly of pyrosequencing reads with mates","volume":"24","author":"Miller","year":"2008","journal-title":"Bioinformatics"},{"key":"2023100601374262400_ref47","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/1748-7188-8-22","article-title":"Space-efficient and exact de Bruijn graph representation based on a bloom filter","volume":"8","author":"Chikhi","year":"2013","journal-title":"Algorithms Mol Biol"},{"key":"2023100601374262400_ref48","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1186\/s13059-020-02134-9","article-title":"Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies","volume":"21","author":"Rhie","year":"2020","journal-title":"Genome Biol"},{"key":"2023100601374262400_ref49","doi-asserted-by":"crossref","first-page":"4647","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes","volume":"38","author":"Manni","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2023100601374262400_ref50","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"2023100601374262400_ref51","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1186\/s12859-021-04118-3","article-title":"Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms","volume":"22","author":"Guiglielmoni","year":"2021","journal-title":"BMC Bioinformatics"},{"key":"2023100601374262400_ref52","doi-asserted-by":"crossref","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation","volume":"44","author":"O\u2019Leary","year":"2016","journal-title":"Nucleic Acids Res"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/6\/bbad337\/51895174\/bbad337.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/6\/bbad337\/51895174\/bbad337.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,6]],"date-time":"2023-10-06T01:40:07Z","timestamp":1696556407000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbad337\/7291993"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,9,22]]},"references-count":52,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2023,9,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbad337","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,11,1]]},"published":{"date-parts":[[2023,9,22]]},"article-number":"bbad337"}}