{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:11:03Z","timestamp":1772165463797,"version":"3.50.1"},"reference-count":47,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2022,2,14]],"date-time":"2022-02-14T00:00:00Z","timestamp":1644796800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2022,2,14]],"date-time":"2022-02-14T00:00:00Z","timestamp":1644796800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31900494"],"award-info":[{"award-number":["31900494"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31730064"],"award-info":[{"award-number":["31730064"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Young Elite Scientists Sponsorship Program by CAST","award":["2019QNRC001"],"award-info":[{"award-number":["2019QNRC001"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2022,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Generating chromosome-scale haplotype resolved assembly is important for functional studies. However, current\n                      <jats:italic>de novo<\/jats:italic>\n                      assemblers are either haploid assemblers that discard allelic information, or diploid assemblers that can only tackle genomes of low complexity.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, Using robust programs, we build a diploid genome assembly pipeline called gcaPDA (gamete cells assisted Phased Diploid Assembler), which exploits haploid gamete cells to assist in resolving haplotypes. We demonstrate the effectiveness of gcaPDA based on simulated HiFi reads of maize genome which is highly heterozygous and repetitive, and real data from rice.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>With applicability of coping with complex genomes and fewer restrictions on application than most of diploid assemblers, gcaPDA is likely to find broad applications in studies of eukaryotic genomes.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-022-04591-4","type":"journal-article","created":{"date-parts":[[2022,2,14]],"date-time":"2022-02-14T07:03:03Z","timestamp":1644822183000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["gcaPDA: a haplotype-resolved diploid assembler"],"prefix":"10.1186","volume":"23","author":[{"given":"Min","family":"Xie","sequence":"first","affiliation":[]},{"given":"Linfeng","family":"Yang","sequence":"additional","affiliation":[]},{"given":"Chenglin","family":"Jiang","sequence":"additional","affiliation":[]},{"given":"Shenshen","family":"Wu","sequence":"additional","affiliation":[]},{"given":"Cheng","family":"Luo","sequence":"additional","affiliation":[]},{"given":"Xin","family":"Yang","sequence":"additional","affiliation":[]},{"given":"Lijuan","family":"He","sequence":"additional","affiliation":[]},{"given":"Shixuan","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Tianquan","family":"Deng","sequence":"additional","affiliation":[]},{"given":"Mingzhi","family":"Ye","sequence":"additional","affiliation":[]},{"given":"Jianbing","family":"Yan","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6354-3534","authenticated-orcid":false,"given":"Ning","family":"Yang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2022,2,14]]},"reference":[{"key":"4591_CR1","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1126\/science.1162986","volume":"323","author":"J Eid","year":"2009","unstructured":"Eid J, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009;323:133\u20138.","journal-title":"Science"},{"key":"4591_CR2","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1373\/clinchem.2014.223016","volume":"61","author":"H Bayley","year":"2015","unstructured":"Bayley H. Nanopore sequencing: from imagination to reality. Clin Chem. 2015;61:25\u201331.","journal-title":"Clin Chem"},{"key":"4591_CR3","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1038\/nbt.2303","volume":"30","author":"ET Lam","year":"2012","unstructured":"Lam ET, et al. Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat Biotechnol. 2012;30:771\u20136.","journal-title":"Nat Biotechnol"},{"key":"4591_CR4","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1126\/science.1181369","volume":"326","author":"E Lieberman-Aiden","year":"2009","unstructured":"Lieberman-Aiden E, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289\u201393.","journal-title":"Science"},{"key":"4591_CR5","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41592-019-0669-3","volume":"17","author":"J Ruan","year":"2020","unstructured":"Ruan J, Li H. Fast and accurate long-read assembly with wtdbg2. Nat Methods. 2020;17:155\u20138.","journal-title":"Nat Methods"},{"key":"4591_CR6","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1038\/nmeth.4432","volume":"14","author":"CL Xiao","year":"2017","unstructured":"Xiao CL, et al. MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. Nat Methods. 2017;14:1072\u20134.","journal-title":"Nat Methods"},{"key":"4591_CR7","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1101\/gr.215087.116","volume":"27","author":"S Koren","year":"2017","unstructured":"Koren S, et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017;27:722\u201336.","journal-title":"Genome Res"},{"key":"4591_CR8","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.csbj.2019.11.011","volume":"18","author":"X Zhang","year":"2020","unstructured":"Zhang X, Wu R, Wang Y, Yu J, Tang H. Unzipping haplotypes in diploid and polyploid genomes. Comput Struct Biotechnol J. 2020;18:66\u201372.","journal-title":"Comput Struct Biotechnol J"},{"key":"4591_CR9","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1038\/nmeth.4035","volume":"13","author":"CS Chin","year":"2016","unstructured":"Chin CS, et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods. 2016;13:1050\u20134.","journal-title":"Nat Methods"},{"key":"4591_CR10","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","volume":"18","author":"H Cheng","year":"2021","unstructured":"Cheng H, Concepcion GT, Feng X, Zhang H, Li H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021;18:170\u20135.","journal-title":"Nat Methods"},{"key":"4591_CR11","doi-asserted-by":"publisher","DOI":"10.1101\/2020.1102.1125.964445","author":"D Heller","year":"2020","unstructured":"Heller D, Vingron M, Church G, Li H, Garg S. SDip: A novel graph-based approach to haplotype-aware assembly based structural variant calling in targeted segmental duplications sequencing. bioRxiv. 2020. https:\/\/doi.org\/10.1101\/2020.1102.1125.964445.","journal-title":"bioRxiv"},{"key":"4591_CR12","doi-asserted-by":"crossref","first-page":"2385","DOI":"10.1093\/bioinformatics\/btz942","volume":"36","author":"S Garg","year":"2020","unstructured":"Garg S, et al. A haplotype-aware de novo assembly of related individuals using pedigree sequence graph. Bioinformatics. 2020;36:2385\u201392.","journal-title":"Bioinformatics"},{"key":"4591_CR13","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1038\/nbt.4277","volume":"36","author":"S Koren","year":"2018","unstructured":"Koren S, et al. De novo assembly of haplotype-resolved genomes with trio binning. Nat Biotechnol. 2018;36:1174\u201382.","journal-title":"Nat Biotechnol"},{"key":"4591_CR14","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/s41587-020-0711-0","volume":"39","author":"S Garg","year":"2021","unstructured":"Garg S, et al. Chromosome-scale, haplotype-resolved assembly of human genomes. Nat Biotechnol. 2021;39:309\u201312.","journal-title":"Nat Biotechnol"},{"key":"4591_CR15","doi-asserted-by":"crossref","first-page":"eabf7117","DOI":"10.1126\/science.abf7117","volume":"372","author":"P Ebert","year":"2021","unstructured":"Ebert P, et al. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science. 2021;372:eabf7117.","journal-title":"Science"},{"key":"4591_CR16","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1186\/s13059-020-02235-5","volume":"21","author":"JA Campoy","year":"2020","unstructured":"Campoy JA, et al. Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes. Genome Biol. 2020;21:306.","journal-title":"Genome Biol"},{"key":"4591_CR17","doi-asserted-by":"crossref","first-page":"1889","DOI":"10.1101\/gr.251033.119","volume":"29","author":"D Shi","year":"2019","unstructured":"Shi D, et al. Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants. Genome Res. 2019;29:1889\u201399.","journal-title":"Genome Res"},{"key":"4591_CR18","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1186\/s12859-018-2485-7","volume":"19","author":"MJ Roach","year":"2018","unstructured":"Roach MJ, Schmidt SA, Borneman AR. Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies. BMC Bioinform. 2018;19:460.","journal-title":"BMC Bioinform"},{"key":"4591_CR19","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41588-018-0182-0","volume":"50","author":"S Sun","year":"2018","unstructured":"Sun S, et al. Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nat Genet. 2018;50:1289\u201395.","journal-title":"Nat Genet"},{"key":"4591_CR20","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1038\/nature22971","volume":"546","author":"Y Jiao","year":"2017","unstructured":"Jiao Y, et al. Improved maize reference genome with single-molecule technologies. Nature. 2017;546:524\u20137.","journal-title":"Nature"},{"key":"4591_CR21","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.1038\/s41588-019-0427-6","volume":"51","author":"N Yang","year":"2019","unstructured":"Yang N, et al. Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement. Nat Genet. 2019;51:1052\u20139.","journal-title":"Nat Genet"},{"key":"4591_CR22","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1101\/gr.180501","volume":"11","author":"FB Dean","year":"2001","unstructured":"Dean FB, Nelson JR, Giesler TL, Lasken RS. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res. 2001;11:1095\u20139.","journal-title":"Genome Res"},{"key":"4591_CR23","doi-asserted-by":"crossref","first-page":"6648","DOI":"10.1038\/ncomms7648","volume":"6","author":"X Li","year":"2015","unstructured":"Li X, Li L, Yan J. Dissecting meiotic recombination based on tetrad analysis by single-microspore sequencing in maize. Nat Commun. 2015;6:6648.","journal-title":"Nat Commun"},{"key":"4591_CR24","doi-asserted-by":"crossref","first-page":"3684","DOI":"10.1093\/molbev\/msaa176","volume":"37","author":"R Li","year":"2020","unstructured":"Li R, et al. Inference of chromosome-length haplotypes using genomic data of three or a few more single gametes. Mol Biol Evol. 2020;37:3684\u201398.","journal-title":"Mol Biol Evol"},{"key":"4591_CR25","doi-asserted-by":"crossref","first-page":"1757","DOI":"10.1016\/j.molp.2021.06.018","volume":"14","author":"JM Song","year":"2021","unstructured":"Song JM, et al. Two gap-free reference genomes and a global view of the centromere architecture in rice. Mol Plant. 2021;14:1757\u201367.","journal-title":"Mol Plant"},{"key":"4591_CR26","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","volume":"31","author":"FA Simao","year":"2015","unstructured":"Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210\u20132.","journal-title":"Bioinformatics"},{"key":"4591_CR27","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1038\/s41588-020-0699-x","volume":"52","author":"Q Zhou","year":"2020","unstructured":"Zhou Q, et al. Haplotype-resolved genome analyses of a heterozygous diploid potato. Nat Genet. 2020;52:1018\u201323.","journal-title":"Nat Genet"},{"key":"4591_CR28","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1038\/s41587-020-0719-5","volume":"39","author":"D Porubsky","year":"2020","unstructured":"Porubsky D, et al. Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. Nat Biotechnol. 2020;39:302\u20138.","journal-title":"Nat Biotechnol"},{"key":"4591_CR29","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1038\/nrg3117","volume":"13","author":"TJ Treangen","year":"2011","unstructured":"Treangen TJ, Salzberg SL. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet. 2011;13:36\u201346.","journal-title":"Nat Rev Genet"},{"key":"4591_CR30","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1038\/nprot.2017.029","volume":"12","author":"AD Sanders","year":"2017","unstructured":"Sanders AD, Falconer E, Hills M, Spierings DCJ, Lansdorp PM. Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs. Nat Protoc. 2017;12:1151\u201376.","journal-title":"Nat Protoc"},{"key":"4591_CR31","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1126\/science.aal3327","volume":"356","author":"O Dudchenko","year":"2017","unstructured":"Dudchenko O, et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science. 2017;356:92\u20135.","journal-title":"Science"},{"key":"4591_CR32","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1105\/tpc.17.00514","volume":"30","author":"JA Udall","year":"2018","unstructured":"Udall JA, Dawe RK. Is it ordered correctly? Validating genome assemblies by optical mapping. Plant Cell. 2018;30:7\u201314.","journal-title":"Plant Cell"},{"key":"4591_CR33","first-page":"11","volume":"19","author":"JJ Doyle","year":"1987","unstructured":"Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull Bot Soc Am. 1987;19:11\u20135.","journal-title":"Phytochem Bull Bot Soc Am"},{"key":"4591_CR34","doi-asserted-by":"crossref","first-page":"101241","DOI":"10.1016\/j.isci.2020.101241","volume":"23","author":"S Gui","year":"2020","unstructured":"Gui S, et al. ZEAMAP, a comprehensive database adapted to the maize multi-omics era. iScience. 2020;23:101241.","journal-title":"iScience"},{"key":"4591_CR35","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-4939-6658-5_1","volume":"1533","author":"DM Bolser","year":"2017","unstructured":"Bolser DM, Staines DM, Perry E, Kersey PJ. Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomic data. Methods Mol Biol. 2017;1533:1\u201331.","journal-title":"Methods Mol Biol"},{"key":"4591_CR36","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, et al. The sequence alignment\/map format and SAMtools. Bioinformatics. 2009;25:2078\u20139.","journal-title":"Bioinformatics"},{"key":"4591_CR37","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1093\/bioinformatics\/bts649","volume":"29","author":"Y Ono","year":"2013","unstructured":"Ono Y, Asai K, Hamada M. PBSIM: PacBio reads simulator\u2013toward accurate genome assembly. Bioinformatics. 2013;29:119\u201321.","journal-title":"Bioinformatics"},{"key":"4591_CR38","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1038\/s41587-019-0217-9","volume":"37","author":"AM Wenger","year":"2019","unstructured":"Wenger AM, et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol. 2019;37:1155\u201362.","journal-title":"Nat Biotechnol"},{"key":"4591_CR39","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1093\/bioinformatics\/btr011","volume":"27","author":"G Marcais","year":"2011","unstructured":"Marcais G, Kingsford C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics. 2011;27:764\u201370.","journal-title":"Bioinformatics"},{"key":"4591_CR40","doi-asserted-by":"crossref","first-page":"2202","DOI":"10.1093\/bioinformatics\/btx153","volume":"33","author":"GW Vurture","year":"2017","unstructured":"Vurture GW, et al. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics. 2017;33:2202\u20134.","journal-title":"Bioinformatics"},{"key":"4591_CR41","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1186\/s13059-015-0831-x","volume":"16","author":"N Servant","year":"2015","unstructured":"Servant N, et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 2015;16:259.","journal-title":"Genome Biol"},{"key":"4591_CR42","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754\u201360.","journal-title":"Bioinformatics"},{"key":"4591_CR43","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","volume":"3","author":"NC Durand","year":"2016","unstructured":"Durand NC, et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 2016;3:95\u20138.","journal-title":"Cell Syst"},{"key":"4591_CR44","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357\u20139.","journal-title":"Nat Methods"},{"key":"4591_CR45","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","volume":"27","author":"H Li","year":"2011","unstructured":"Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011;27:2987\u201393.","journal-title":"Bioinformatics"},{"key":"4591_CR46","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1186\/s13059-020-02134-9","volume":"21","author":"A Rhie","year":"2020","unstructured":"Rhie A, Walenz BP, Koren S, Phillippy AM. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020;21:245.","journal-title":"Genome Biol"},{"key":"4591_CR47","doi-asserted-by":"crossref","first-page":"e1005944","DOI":"10.1371\/journal.pcbi.1005944","volume":"14","author":"G Marcais","year":"2018","unstructured":"Marcais G, et al. MUMmer4: a fast and versatile genome alignment system. PLoS Comput Biol. 2018;14:e1005944.","journal-title":"PLoS Comput Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-022-04591-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-022-04591-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-022-04591-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,2,14]],"date-time":"2022-02-14T07:11:38Z","timestamp":1644822698000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-022-04591-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2,14]]},"references-count":47,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2022,12]]}},"alternative-id":["4591"],"URL":"https:\/\/doi.org\/10.1186\/s12859-022-04591-4","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.05.31.446328","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,2,14]]},"assertion":[{"value":"21 December 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 January 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 February 2022","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"M.X., L-F.Y., X.Y., L-J.H., S-X.C., T-Q.D. and M-Z.Y. are employees of BGI-Shenzhen. The gcaPDA methodology are covered in pending patents.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"68"}}