Eggertsson HP, Jonsson H, Kristmundsdottir S, Hjartarson E, Kehr B, Masson G, Zink F, Hjorleifsson KE, Jonasdottir A, Jonasdottir A, et al. Graphtyper enables population-scale genotyping using pangenome graphs. Nat Genet. 2017;49:1654.
Article
CAS
Google Scholar
Shi L, Guo Y, Dong C, Huddleston J, Yang H, Han X, Fu A, Li Q, Li N, Gong S, et al. Long-read sequencing and de novo assembly of a Chinese genome. Nat Commun. 2016;7:12065.
Article
CAS
Google Scholar
Li R, Li Y, Zheng H, Luo R, Zhu H, Li Q, Qian W, Ren Y, Tian G, Li J, et al. Building the sequence map of the human pan-genome. Nat Biotechnol. 2010;28:57–63.
Article
CAS
Google Scholar
Kehr B, Helgadottir A, Melsted P, Jonsson H, Helgason H, Jonasdottir A, Jonasdottir A, Sigurdsson A, Gylfason A, Halldorsson GH, et al. Diversity in non-repetitive human sequences not found in the reference genome. Nat Genet. 2017;49:588.
Article
CAS
Google Scholar
Altshuler DM, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, Clark AG, Donnelly P, Eichler EE, Flicek P, Gabriel SB, et al. A global reference for human genetic variation. Nature. 2015;526:68.
Article
CAS
Google Scholar
Telenti A, Pierce LCT, Biggs WH, di Iulio J, Wong EHM, Fabani MM, Kirkness EF, Moustafa A, Shah N, Xie C, et al. Deep sequencing of 10,000 human genomes. Proc Natl Acad Sci U S A. 2016;113:11901–6.
Article
CAS
Google Scholar
Wong KHY, Levy-Sakin M, Kwok PY. De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations. Nat Commun. 2018;9:3040.
Article
Google Scholar
Faber-Hammond JJ, Brown KH. Anchored pseudo-de novo assembly of human genomes identifies extensive sequence variation from unmapped sequence reads. Hum Genet. 2016;135:727–40.
Article
Google Scholar
Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao MY, Chennagiri N, Nordenfelt S, Tandon A, et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. 2016;538:201.
Article
CAS
Google Scholar
Vernikos G, Medini D, Riley DR, Tettelin H. Ten years of pan-genome analyses. Curr Opin Microbiol. 2015;23:148–54.
Article
CAS
Google Scholar
Mongodin EF, Casjens SR, Bruno JF, Xu Y, Drabek EF, Riley DR, Cantarel BL, Pagan PE, Hernandez YA, Vargas LC, et al. Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation. BMC Genomics. 2013;14:693.
Article
CAS
Google Scholar
Sun C, Hu ZQ, Zheng TQ, Lu KC, Zhao Y, Wang WS, Shi JX, Wang CC, Lu JY, Zhang DB, et al. RPAN: rice pan-genome browser for similar to 3000 rice genomes. Nucleic Acids Res. 2017;45:597–605.
Article
CAS
Google Scholar
Wang WS, Mauleon R, Hu ZQ, Chebotarov D, Tai SS, Wu ZC, Li M, Zheng TQ, Fuentes RR, Zhang F, et al. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature. 2018;557:43.
Article
CAS
Google Scholar
Li YH, Zhou GY, Ma JX, Jiang WK, Jin LG, Zhang ZH, Guo Y, Zhang JB, Sui Y, Zheng LT, et al. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat Biotechnol. 2014;32:1045.
Article
CAS
Google Scholar
Hirsch CN, Foerster JM, Johnson JM, Sekhon RS, Muttoni G, Vaillancourt B, Penagaricano F, Lindquist E, Pedraza MA, Barry K, et al. Insights into the maize pan-genome and pan-transcriptome. Plant Cell. 2014;26:121–35.
Article
CAS
Google Scholar
Zhao Q, Feng Q, Lu H, Li Y, Wang A, Tian Q, Zhan Q, Lu Y, Zhang L, Huang T, et al. Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nat Genet. 2018;50:278–84.
Article
CAS
Google Scholar
Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial ‘pan-genome’. Proc. Natl. Acad. Sci. U. S. A. 2005;102:16530.
Article
CAS
Google Scholar
Marroni F, Pinosio S, Morgante M. Structural variation and genome complexity: is dispensable really dispensable? Curr Opin Plant Biol. 2014;18:31–6.
Article
CAS
Google Scholar
Besenbacher S, Liu SY, Izarzugaza JMG, Grove J, Belling K, Bork-Jensen J, Huang SJ, Als TD, Li ST, Yadav R, et al. Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios. Nat Commun. 2015;6:5969.
Sherman RM, Forman J, Antonescu V, Puiu D, Daya M, Rafaels N, Boorgula MP, Chavan S, Vergara C, Ortega VE, et al. Assembly of a pan-genome from deep sequencing of 910 humans of African descent. Nat Genet. 2019;51:30.
Article
Google Scholar
Maretty L, Jensen JM, Petersen B, Sibbesen JAN, Liu SY, Villesen P, Kov LS, Belling K, Have CTH, Izarzugaza JMG, et al. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nature. 2017;548:87.
Article
CAS
Google Scholar
Hu Z, Sun C, Lu KC, Chu X, Zhao Y, Lu J, Shi J, Wei C. EUPAN enables pan-genome studies of a large number of eukaryotic genomes. Bioinformatics. 2017;33:2408–9.
Article
CAS
Google Scholar
Lan TM, Lin HX, Zhu WJ, Laurent TCAM, Yang MC, Liu X, Wang J, Wang J, Yang HM, Xu X, Guo XS. Deep whole-genome sequencing of 90 Han Chinese genomes. Gigascience. 2017;6(9):1–7.
Simpson JT, Durbin R. Efficient de novo assembly of large genomes using compressed data structures. Genome Res. 2012;22:549–56.
Article
CAS
Google Scholar
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, et al: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2012;1:18.
Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J, et al. The diploid genome sequence of an Asian individual. Nature. 2008;456:60–5.
Article
CAS
Google Scholar
Istrail S, Sutton GG, Florea L, Halpern AL, Mobarry CM, Lippert R, Walenz B, Shatkay H, Dew I, Miller JR, et al. Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci U S A. 2004;101:1916–21.
Article
CAS
Google Scholar
Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, et al. The diploid genome sequence of an individual human. PLoS Biol. 2007;5:e254.
Article
Google Scholar
Seo JS, Rhie A, Kim J, Lee S, Sohn MH, Kim CU, Hastie A, Cao H, Yun JY, Kim J, et al. De novo assembly and phasing of a Korean human genome. Nature. 2016;538:243–7.
Article
CAS
Google Scholar
Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018;36:338–45.
Article
CAS
Google Scholar
McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB, Lee C, Daly MJ, et al. Common deletion polymorphisms in the human genome. Nat Genet. 2006;38:86–92.
Article
CAS
Google Scholar
Alkan C, Sajjadian S, Eichler EE. Limitations of next-generation genome sequence assembly. Nat Methods. 2011;8:61–5.
Article
CAS
Google Scholar
Lee I, Chalita M, Ha SM, Na SI, Yoon SH, Chun J. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol. 2017;67:2053–7.
Article
CAS
Google Scholar
Sedlazeck FJ, Lee H, Darby CA, Schatz MC. Piercing the dark matter: bioinformatics of long-range sequencing and mapping. Nat Rev Genet. 2018;19:329–46.
Article
CAS
Google Scholar
Gurevich A, Saveliev V, Vyahhi N, Tesler G: QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29:1072–1075.
Article
CAS
Google Scholar
Fu L, Niu B, Zhu Z, Wu S, Li W: CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28:3150–3152.
Article
CAS
Google Scholar
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012;22:1760–74.
Article
CAS
Google Scholar
Holt C, Yandell M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics. 2011;12:491.
Article
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–359.
Article
CAS
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S: The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078–2079.
Article
Google Scholar
Duan Z, Qiao Y, Lu J, Lu H, Zhang W, Yan F, Sun C, Hu Z, Zhang Z, Li G, et al. HUPAN: a pan-genome analysis pipeline for human genomes. GitHub Repository 2019. https://github.com/SJTU-CGM/HUPAN.
Duan Z, Qiao Y, Lu J, Lu H, Zhang W, Yan F, Sun C, Hu Z, Zhang Z, Li G, et al: HUPAN: a pan-genome analysis pipeline for human genomes. Zenodo Repository 2019. https://doi.org/10.5281/zenodo.2593453.
Duan Z, Qiao Y, Lu J, Lu H, Zhang W, Yan F, Sun C, Hu Z, Zhang Z, Li G, et al: HUPAN: a pan-genome analysis pipeline for human genomes. European Genome-phenome Archive (EGA) 2019. https://www.ebi.ac.uk/ega/studies/EGAS00001003657.
Duan Z, Qiao Y, Lu J, Lu H, Zhang W, Yan F, Sun C, Hu Z, Zhang Z, Li G, et al: HUPAN: a pan-genome analysis pipeline for human genomes. The National Omics Data Encyclopedia (NODE) 2019. https://www.biosino.org/node/project/detail/OEP000301.
Mikkelsen TS, Hillier LW, Eichler EE, Zody MC, Jaffe DB, Yang SP, Enard W, Hellmann I, Lindblad-Toh K, Altheide TK, et al. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 2005;437:69–87.
Article
CAS
Google Scholar
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, et al. Insights into hominid evolution from the gorilla genome sequence. Nature. 2012;483:169–75.
Article
CAS
Google Scholar
Prufer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, et al. The bonobo genome compared with the chimpanzee and human genomes. Nature. 2012;486:527–31.
Article
Google Scholar
Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang ZY, Chinwalla AT, Minx P, et al. Comparative and demographic analysis of orang-utan genomes. Nature. 2011;469:529–33.
Article
CAS
Google Scholar
Zimin AV, Cornish AS, Maudhoo MD, Gibbs RM, Zhang X, Pandey S, Meehan DT, Wipfler K, Bosinger SE, Johnson ZP, et al. A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biol Direct. 2014;9(1):20.
Rogers J, Raveendran M, Harris RA, Mailund T, Leppala K, Athanasiadis G, Schierup MH, Cheng J, Munch K, Walker JA, et al. The comparative genomics and complex population history of Papio baboons. Sci Adv. 2019;5:eaau6947.
Article
Google Scholar