<\/p>\n
Chaisson, MJ et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat. Commun.<\/i> 10<\/b>1\u201316 (2019).<\/p>\n
Article Google Scholar\n <\/p>\n<\/li>\n
Conesa, A. et al. A survey of best practices for RNA-seq data analysis. Genome Biol.<\/i> 17<\/b>1\u201319 (2016).<\/p>\n
Article Google Scholar\n <\/p>\n<\/li>\n
Beyter, D. et al. Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits. Nat. Genet.<\/i> 53<\/b>779\u2013886 (2021).<\/p>\n<\/li>\n Rhie, A. et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature<\/i> 592<\/b>737\u2013746 (2021).<\/p>\n Article Google Scholar\n <\/p>\n<\/li>\n De Coster, W., Weissensteiner, MH & Sedlazeck, FJ Towards population-scale long-read sequencing. Nat. Rev. Genet.<\/i> 22<\/b>572\u2013587 (2021).<\/p>\n<\/li>\n Promethion Brochure<\/i> (Nanophore Technologies, 2021); https:\/\/nanoporetech.com\/sites\/default\/files\/s3\/literature\/PromethION-brochure.pdf<\/p>\n<\/li>\n Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics<\/i> 34<\/b>3094\u20133100 (2018).<\/p>\n Article Google Scholar\n <\/p>\n<\/li>\n Guo, L., Lau, J., Ruan, Z., Wei, P. & Cong, J. Hardware acceleration of long read pairwise overlapping in genome sequencing: a race between FPGA and GPU. In 2019 IEEE 27th Annual International Symposium on Field-Programmable Custom Computing Machines<\/i> 127\u2013135 (IEEE, 2019).<\/p>\n<\/li>\n Zeni, A. et al. LOGAN: high-performance GPU-based X-drop long-read alignment. In 2020 IEEE International Parallel and Distributed Processing Symposium<\/i> 462\u2013471 (IEEE, 2020).<\/p>\n<\/li>\n Feng, Z., Qiu, S., Wang, L. & Luo, Q. Accelerating long read alignment on three processors. In Proc. 48th International Conference on Parallel Processing<\/i> 1\u201310 (ACM, 2019).<\/p>\n<\/li>\n Roberts, M., Hayes, W., Hunt, BR, Mount, SM & Yorke, JA Reducing storage requirements for biological sequence comparison. Bioinformatics<\/i> 20<\/b>3363\u20133369 (2004).<\/p>\n Article Google Scholar\n <\/p>\n<\/li>\n Abouelhoda, MI & Ohlebusch, E. Chaining algorithms for multiple genome comparison. J. Discrete Algorithms<\/i> 3<\/b>321\u2013341 (2005).<\/p>\n MathSciNet Article Google Scholar\n <\/p>\n<\/li>\n Jain, C., Gibney, D. & Thankachan, SV Co-linear chaining with overlaps and gap costs. Preprint at https:\/\/www.biorxiv.org\/content\/10.1101\/2021.02.03.429492v2 (2021).<\/p>\n<\/li>\n Ho, D. et al. LISA: learned indexes for DNA sequence analysis. Preprint at https:\/\/arxiv.org\/abs\/1910.04728 (2020).<\/p>\n<\/li>\n Schneider, VA et al. Evaluation of GRCh38 and de novo haploid genome assembly demonstrates the enduring quality of the reference assembly. Genome Res.<\/i> 27<\/b>849\u2013864 (2017).<\/p>\n Article Google Scholar\n <\/p>\n<\/li>\n Nurk, S., Koren, S., Rhie, A., Rautiainen, M. et al. The complete sequence of a human genome. Preprint at https:\/\/doi.org\/10.1101\/2021.05.26.445798 (2021).<\/p>\n<\/li>\n Cheng, H., Concepcion, GT, Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods<\/i> 18<\/b>170\u2013175 (2021).<\/p>\n Article Google Scholar\n <\/p>\n<\/li>\n Payne, A. et al. Readfish enables targeted nanopore sequencing of gigabase-sized genomes. Nat. Biotechnol.<\/i> 39<\/b>442\u2013450 (2021).<\/p>\n Article Google Scholar\n <\/p>\n<\/li>\n Kovaka, S., Fan, Y., Ni, B., Timp, W. & Schatz, MC Targeted nanopore sequencing by real-time mapping of raw electrical signal with uncalled. Nat. Biotechnol.<\/i> 39<\/b>431\u2013441 (2021).<\/p>\n Article Google Scholar\n <\/p>\n<\/li>\n Zhang, H. et al. Real-time mapping of nanopore raw signals. Bioinformatics<\/i> https:\/\/doi.org\/10.1093\/bioinformatics\/btab264 (2021).<\/p>\n<\/li>\n Jain, C., Rhie, A., Hansen, N., Koren, S. & Phillippy, AM A long read mapping method for highly repetitive reference sequences. Preprint at https:\/\/www.biorxiv.org\/content\/10.1101\/2020.11.01.363887v1.full (2020).<\/p>\n<\/li>\n Sedlazeck, FJ et al. Accurate detection of complex structural variations using single-molecule sequencing. Nat. Methods<\/i> 15th<\/b>461\u2013468 (2018).<\/p>\n Article Google Scholar\n <\/p>\n<\/li>\n Ren, J. & Chaisson, M. lRA: the long read aligner for sequences and contigs. Preprint at https:\/\/doi.org\/10.1371\/journal.pcbi.1009078 (2020).<\/p>\n<\/li>\n Kraska, T., Beutel, A., Chi, EH, Dean, J. & Polyzotis, N. The case for learned index structures. In ACM International Conference on Management of Data<\/i> 489\u2013504 (ACM, 2018).<\/p>\n<\/li>\n Galakatos, A., Markovitch, M., Binnig, C., Fonseca, R. & Kraska, T. FITing-Tree: a data-aware index structure. In SIGMOD ’19: Proceedings of the 2019 International Conference on Management of Data<\/i> 1189\u20131206 (ACM, 2019); https:\/\/doi.org\/10.1145\/3299869.3319860<\/p>\n<\/li>\n Ferragina, P. & Vinciguerra, G. The PGM-index: a fully-dynamic compressed learned index with provable worst-case bounds. PVLDB<\/i> 13<\/b>1162\u20131175 (2020).<\/p>\n \n Google Scholar\n <\/p>\n<\/li>\n Ding, J. et al. ALEX: An Updatable Adaptive Learned Index. In SIGMOD ’20: Proceedings of the 2020 International Conference on Management of Data<\/i> 969-984 (ACM, 2020). https:\/\/doi.org\/10.1145\/3318464.3389711<\/p>\n<\/li>\n Wu, Y., Yu, J., Tian, \u200b\u200bY., Sidle, R. & Barber, R. Designing succinct secondary indexing mechanism by exploiting column correlations. In SIGMOD ’19: Proceedings of the 2019 International Conference on Management of Data<\/i> 1223\u20131240 (ACM, 2019). https:\/\/doi.org\/10.1145\/3299869.3319861<\/p>\n<\/li>\n Kirsche, M., Das, A. & Schatz, MC Sapling: accelerating suffix array queries with learned data models. Bioinformatics<\/i> 37<\/b>744\u2013749 (2021).<\/p>\n Article Google Scholar\n <\/p>\n<\/li>\n Marcus, R. et al. Benchmarking learned indexes. In PVLDB<\/i> Vol. 14, 1\u201313 (2021).<\/p>\n<\/li>\n Marcus, R., Zhang, E. & Kraska, T. CDFShop: exploring and optimizing learned index structures. In SIGMOD ’20:<\/i> Proc. 2020 ACM SIGMOD International Conference on Management of Data<\/i> 2789\u20132792 (ACM, 2020); https:\/\/doi.org\/10.1145\/3318464.3384706<\/p>\n<\/li>\n Suzuki, H. & Kasahara, M. Introducing difference recurrence relations for faster semi-global alignment of long sequences. BMC Bioinformatics<\/i> 19<\/b>33\u201347 (2018).<\/p>\n Article Google Scholar\n <\/p>\n<\/li>\n Cheng, H., Concepcion, G., Feng, X., Zhang, H. & Li, H. Human Assemblies Evaluated in the Hifiasm Paper<\/i> (Zenodo, 2020); https:\/\/doi.org\/10.5281\/zenodo.4393631<\/p>\n<\/li>\n Kalikar, S., Jain, C., Md, V. & Misra, S. mm2-fast Source Code Used in the Manuscript\u2014Accelerating Minimap2 for Long-Read Sequencing Applications on Modern CPUs<\/i> (Zenodo, 2022); https:\/\/doi.org\/10.5281\/zenodo.5888171<\/p>\n<\/li>\n Kalikar, S., Jain, C., Md, V. & Misra, S. Scripts Used for the Experiments in the Manuscript\u2014Accelerating Minimap2 for Long-Read Sequencing Applications on Modern CPUs<\/i> (Zenodo, 2022); https:\/\/doi.org\/10.5281\/zenodo.5884451<\/p>\n<\/li>\n<\/div>\n","protected":false},"excerpt":{"rendered":" Chaisson, MJ et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat. Commun. 101\u201316 (2019). Article Google Scholar…<\/span><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3],"tags":[],"class_list":["post-7502","post","type-post","status-publish","format-standard","hentry","category-architecture","no-post-thumbnail"],"_links":{"self":[{"href":"https:\/\/wijhha.com\/index.php\/wp-json\/wp\/v2\/posts\/7502","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wijhha.com\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/wijhha.com\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/wijhha.com\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/wijhha.com\/index.php\/wp-json\/wp\/v2\/comments?post=7502"}],"version-history":[{"count":0,"href":"https:\/\/wijhha.com\/index.php\/wp-json\/wp\/v2\/posts\/7502\/revisions"}],"wp:attachment":[{"href":"https:\/\/wijhha.com\/index.php\/wp-json\/wp\/v2\/media?parent=7502"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/wijhha.com\/index.php\/wp-json\/wp\/v2\/categories?post=7502"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/wijhha.com\/index.php\/wp-json\/wp\/v2\/tags?post=7502"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}