[1] 朱晓.基于高能量测序数据的基因组拼接方法研究[D].哈尔滨:哈尔滨工业大学,2015. ZHU X.Study on genomic splicing method based on high-energy sequencing data[D].Harbin:Harbin Institute of Technology,2015.(in Chinese) [2] 郭睿.基于长读的基因组重复序列查找技术研究[D].深圳:深圳大学,2018. GUO R.Research on genomic repeat sequence searching technology based on long reads[D].Shenzhen:Shenzhen University,2018.(in Chinese) [3] ZHU B H.Genomic scaffold filling:a progress report[C]//Proceedings of International Workshop on Frontiers in Algorithmics.Berlin,Germany:Springer,2016:8-16. [4] RHOADS A,AU K F.PacBio sequencing and its applications[J].Genomics,Proteomics & Bioinformatics,2015,13(5):278-289. [5] LU H,GIORDANO F,NING Z.Oxford Nanopore MinION sequencing and genome assembly[J].Genomics,Proteomics & Bioinformatics,2016,14(5):265-279. [6] TSAI I J,OTTO T D,BERRIMAN M.Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps[J].Genome Biology,2010,11(4):41. [7] ZERBINO D R.Using the velvet de novo assembler for short-read sequencing technologies[J].Current Protocols in Bioinformatics,2010,31(1):1-12. [8] LI R,ZHU H,RUAN J,et al.De novo assembly of human genomes with massively parallel short read sequencing[J].Genome Research,2010,20(2):265-272. [9] SCHATZ M,DELCHER A L,SALZBERG S L.Assembly of large genomes using cloud computing[J].Genome Research,2010,20(9):1165-1173. [10] BOETZER M,PIROVANO W.Toward almost closed genomes with gap filler[J].Genome Biology,2012,13(6):56. [11] GAO S,BERTRAND D,NAGARAJAN N.FinIS:improved in silico finishing using an exact quadratic programming formulation[C]//Proceedings of International Workshop on Algorithms in Bioinformatics.Berlin,Germany:Springer,2012:314-325. [12] PAULINO D,WARREN R L,VANDERVALK B P,et al.Sealer:a scalable gap-closing application for finishing draft genomes[J].BMC Bioinformatics,2015,16(1):230. [13] SALMELA L,SAHLIN K,MAKINEN V,et al.Gap filling as exact path length problem[J].Journal of Computational Biology,2016,23(5):347-361. [14] LUO J W,WANG J X,SHANG J,et al.GapReduce:a gap filling algorithm based on partitioned read sets[J].IEEE/ACM Transactions on Computational Biology and Bioinformatics,2020,17(3):877-886. [15] ENGLISH A C,RICHARDS S,HAN Y,et al.Mind the gap:upgrading genomes with Pacific Biosciences RS long-read sequencing technology[J].PLoS One,2012,7(11):477-488. [16] CHAISSON M J,TESLER G.Mapping single molecule sequencing reads using basic local alignment with successive refinement:application and theory[J].BMC Bioinformatics,2012,13(1):238. [17] 买阿丽,杨雯雯.关于基因重组中OLC算法的改进研究[J].郑州大学学报(理学版),2016,48(2):34-39. MAI A L,YANG W W.Research on improvement of OLC algorithm in gene recombination[J].Journal of Zhengzhou University(Science Edition),2016,48(2):34-39.(in Chinese) [18] SENOL C D,KIM J S,GHOSE S,et al.Nanopore sequencing technology and tools for genome assembly:computational analysis of the current state,bottlenecks and future directions[J].Briefings in Bioinformatics,2019,20(4):1542-1559. [19] KOSUGI S,HIRAKAWA H,TABATA S.GMcloser:closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments[J].Bioinformatics,2015,31(23):3733-3741. [20] XU G C,XU T J,ZHU R,et al.LR_Gapcloser:a tiling path-based gap closer that uses long reads to complete genome assembly[J].Giga Science,2019,8(1):157-169. [21] LI H.Aligning sequence reads,clone sequences and assembly contigs with BWA-MEM[EB/OL].[2020-09-10].https://arxiv.org/pdf/303.3997.pdf. [22] VASER R,SOVIE I,NAGARAJAN N,et al.Racon-rapid consensus module for raw de novo genome assembly of long uncorrected reads[J].Bioinformatics,2002,18(10):452-464. [23] LI H.Minimap2:pairwise alignment for nucleotide sequences[J].Bioinformatics,2018,34(18):3094-3100. [24] KATOH K,MISAWA K,KUMA K,et al.MAFFT:a novel method for rapid multiple sequence alignment based on fast Fourier transform[J].Nucleic Acids Research,2002,30(14):3059-3066. [25] GUREVICH A,SAVELIEV V,VYAHHI N,et al.QUAST:quality assessment tool for genome assemblies[J].Bioinformatics,2013,29(8):1072-1075. [26] KOREN S,WALENZ B P,BERLIN K,et al.Canu:scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation[J].Genome Research,2017,27(5):722-736. |