期刊文献+

Single-Molecule Sequencing Assists Genome Assembly Improvement and Structural Variation Inference 被引量:1

Single-Molecule Sequencing Assists Genome Assembly Improvement and Structural Variation Inference
原文传递
导出
摘要 The single-molecule real-time (SMRT) sequencing platform pre- sented by Pacific Biosciences (PacBio) is regarded as a third- generation sequencing technology (Eid et al, 2009; Roberts et al., 2013). PacBio delivers long reads from several to tens of kilobases (kbs), which are ideal for filling unsequenced gaps due to unusual sequence contexts, such as high^GC content or repeat-rich regions (Bashir et al., 2012; Berlin et al., 2015; Chaisson et al., 2015). PacBio long reads are also favorable for detecting large DNA fragments harboring structural variations (SVs), such as inversions, translocations, duplications, and large insertions/deletions (indels) (Ritz et al., 2010; English et al., 2014). The single-molecule real-time (SMRT) sequencing platform pre- sented by Pacific Biosciences (PacBio) is regarded as a third- generation sequencing technology (Eid et al, 2009; Roberts et al., 2013). PacBio delivers long reads from several to tens of kilobases (kbs), which are ideal for filling unsequenced gaps due to unusual sequence contexts, such as high^GC content or repeat-rich regions (Bashir et al., 2012; Berlin et al., 2015; Chaisson et al., 2015). PacBio long reads are also favorable for detecting large DNA fragments harboring structural variations (SVs), such as inversions, translocations, duplications, and large insertions/deletions (indels) (Ritz et al., 2010; English et al., 2014).
出处 《Molecular Plant》 SCIE CAS CSCD 2016年第7期1085-1087,共3页 分子植物(英文版)
  • 相关文献

参考文献12

  • 1Au, K.F., Underwood, J.G., Lee, L., and Wong, W.H. (2012). Improving PacBio long read accuracy by short read alignment. PLoS One 7:e46679.
  • 2Bashir, A., Klammer, A.A., Robins, WoP., Chin, C.S., Webster, D., Paxinos, E., Hsu, D., Ashby, M., Wang, S., Peluso, P., et al. (2012). A hybrid approach for the automated finishing Of bacterial genomes. Nat. Biotechnol. 30:701-707.
  • 3Berlin, K., Koren, S., Chin, C.S., Drake, J.P., Landolin, J.M., and Phillippy, A.M. (2015). Assembling large genomes with single- molecule sequencing and locality-sensitive hashing. Nat. Biotechnol. 33:623-630.
  • 4Chaisson, M.J., and Tesler, G. (2012). Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 13:238.
  • 5Chaisson, M.J., Huddleston, J., Dennis, M.Y., Sudmant, P.H., Malig, M., Hormozdiari, F., Antonacci, F., Surti, U., Sandstrom, R., Boitano, M., et al. (2015). Resolving the complexity of the human genome using single-molecule sequencing. Nature 517:608-611.
  • 6Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B., et al. (2009). Real-time DNA sequencing from single polymerase molecules. Science 323:133-138.
  • 7English, A.C., Richards, S., Hart, Y., Wang, M., Vee, V., Qu, J., Qin, X., Muzny, D.M., Reid, J.G., Worley, K.C., et al. (2012). Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One 7:e47768.
  • 8English, A.C., Salerno, W.J., and Reid, J.G. (2014). PBHoney: identifying genomic variants via long-read discordance and interrupted mapping. BMC Bioinformatics 15:180.
  • 9Jacquemin, J., Bhatia, D., Singh, K., and Wing, R,A. (2013). The International Oryza Map Alignment Project: development of a genus- wide comparative genomics platform to help solve the 9 billion- people question. Curr. Opin. Plant Biol. 16:147-156.
  • 10Koren, S., Schatz, M.C., Walenz, B.P., Martin, J., Howard, J.T., Ganapathy, G., Wang, Z., Rasko, D.A., McCombie, W.R., Jarvis, E.D., et al, (2012). Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat. Biotechnol. 30:693-700.

同被引文献4

引证文献1

二级引证文献1

相关作者

内容加载中请稍等...

相关机构

内容加载中请稍等...

相关主题

内容加载中请稍等...

浏览历史

内容加载中请稍等...
;
使用帮助 返回顶部