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Volumn 16, Issue 1, 2015, Pages

Circlator: Automated circularization of genome assemblies using long sequencing reads

Author keywords

Assembly; Circularization

Indexed keywords

CONTIG; CIRCULAR DNA;

EID: 84951969455     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-015-0849-0     Document Type: Article
Times cited : (777)

References (31)
  • 1
    • 0018426987 scopus 로고
    • A strategy of DNA sequencing employing computer programs
    • Staden R. A strategy of DNA sequencing employing computer programs. Nucleic Acids Res. 1979; 6(7):2601-10. doi: 10.1093/nar/gkq840.
    • (1979) Nucleic Acids Res , vol.6 , Issue.7 , pp. 2601-2610
    • Staden, R.1
  • 2
    • 84913554630 scopus 로고    scopus 로고
    • One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly
    • Koren S, Phillippy AM. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr Opin Microbiol. 2015; 23:110-20. doi: 10.1016/j.mib.2014.11.014.
    • (2015) Curr Opin Microbiol , vol.23 , pp. 110-120
    • Koren, S.1    Phillippy, A.M.2
  • 3
    • 84880798154 scopus 로고    scopus 로고
    • Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
    • Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al.Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods. 2013; 10(6):563-9. doi: 10.1038/nmeth.2474.
    • (2013) Nat Methods , vol.10 , Issue.6 , pp. 563-569
    • Chin, C.S.1    Alexander, D.H.2    Marks, P.3    Klammer, A.A.4    Drake, J.5    Heiner, C.6
  • 4
    • 84930851165 scopus 로고    scopus 로고
    • Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
    • Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol. 2015; 33(6):623-30. doi: 10.1038/nbt.3238.
    • (2015) Nat Biotechnol , vol.33 , Issue.6 , pp. 623-630
    • Berlin, K.1    Koren, S.2    Chin, C.S.3    Drake, J.P.4    Landolin, J.M.5    Phillippy, A.M.6
  • 5
    • 84951938472 scopus 로고    scopus 로고
    • Single pass read accuracy improver
    • Accessed 19 Nov
    • SPRAI: Single pass read accuracy improver. http://zombie.cb.k.u-tokyo.ac.jp/sprai/index.html. Accessed 19 Nov 2014.
    • (2014)
  • 6
    • 84862318037 scopus 로고    scopus 로고
    • A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance
    • Eyre DW, Golubchik T, Gordon NC, Bowden R, Piazza P, Batty EM, et al.A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance. BMJ Open. 2012; 2(3):001124. doi: 10.1136/bmjopen-2012-001124.
    • (2012) BMJ Open , vol.2 , Issue.3 , pp. 001124
    • Eyre, D.W.1    Golubchik, T.2    Gordon, N.C.3    Bowden, R.4    Piazza, P.5    Batty, E.M.6
  • 8
    • 42449146057 scopus 로고    scopus 로고
    • Mitochondrial involvement in psychiatric disorders
    • Shao L, Martin MV, Watson SJ, Schatzberg A, Akil H, Myers RM, et al.Mitochondrial involvement in psychiatric disorders. Ann Med. 2008; 40(4):281-95. doi: 10.1080/07853890801923753.
    • (2008) Ann Med , vol.40 , Issue.4 , pp. 281-295
    • Shao, L.1    Martin, M.V.2    Watson, S.J.3    Schatzberg, A.4    Akil, H.5    Myers, R.M.6
  • 9
    • 84929023781 scopus 로고    scopus 로고
    • Molecular signatures of major depression
    • Cai N, Chang S, Li Y, Li Q, Hu J, Liang J, et al.Molecular signatures of major depression. Curr Biol. 2015; 25:1146-1156. doi: 10.1016/j.cub.2015.03.008.
    • (2015) Curr Biol , vol.25 , pp. 1146-1156
    • Cai, N.1    Chang, S.2    Li, Y.3    Li, Q.4    Hu, J.5    Liang, J.6
  • 10
    • 34547796899 scopus 로고    scopus 로고
    • Clinical expression of Leber hereditary optic neuropathy is affected by the mitochondrial DNA-haplogroup background
    • Hudson G, Carelli V, Spruijt L, Gerards M, Mowbray C, Achilli A, et al.Clinical expression of Leber hereditary optic neuropathy is affected by the mitochondrial DNA-haplogroup background. Am J Hum Genet. 2007; 81(2):228-33. doi: 10.1086/519394.
    • (2007) Am J Hum Genet , vol.81 , Issue.2 , pp. 228-233
    • Hudson, G.1    Carelli, V.2    Spruijt, L.3    Gerards, M.4    Mowbray, C.5    Achilli, A.6
  • 11
    • 0028927272 scopus 로고
    • Segregation patterns of a novel mutation in the mitochondrial tRNA glutamic acid gene associated with myopathy and diabetes mellitus
    • Hao H, Bonilla E, Manfredi G, DiMauro S, Moraes CT. Segregation patterns of a novel mutation in the mitochondrial tRNA glutamic acid gene associated with myopathy and diabetes mellitus. Am J Hum Genet. 1995; 56(5):1017-25.
    • (1995) Am J Hum Genet , vol.56 , Issue.5 , pp. 1017-1025
    • Hao, H.1    Bonilla, E.2    Manfredi, G.3    DiMauro, S.4    Moraes, C.T.5
  • 14
    • 84952055055 scopus 로고    scopus 로고
    • Accessed 28 Jul
    • NCTC 3000 Project. https://www.phe-culturecollections.org.uk/collections/nctc-3000-project.aspx. Accessed 28 Jul 2015.
    • (2015)
  • 15
    • 84938421951 scopus 로고    scopus 로고
    • A complete bacterial genome assembled de novo using only nanopore sequencing data
    • Loman NJ, Quick J, Simpson JT. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods. 2015; 12(8):733-735. doi: 10.1038/nmeth.3444.
    • (2015) Nat Methods , vol.12 , Issue.8 , pp. 733-735
    • Loman, N.J.1    Quick, J.2    Simpson, J.T.3
  • 16
    • 84876266928 scopus 로고    scopus 로고
    • QUAST: quality assessment tool for genome assemblies
    • Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013; 29(8):1072-5. doi: 10.1093/bioinformatics/btt086.
    • (2013) Bioinformatics , vol.29 , Issue.8 , pp. 1072-1075
    • Gurevich, A.1    Saveliev, V.2    Vyahhi, N.3    Tesler, G.4
  • 17
    • 84857893016 scopus 로고    scopus 로고
    • GAGE: a critical evaluation of genome assemblies and assembly algorithms
    • Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, et al.GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res. 2012; 22(3):557-67. doi:doi:10.1101/gr.131383.11110.1101/gr.131383.111 10.1101/gr.131383.111.
    • (2012) Genome Res , vol.22 , Issue.3 , pp. 557-567
    • Salzberg, S.L.1    Phillippy, A.M.2    Zimin, A.3    Puiu, D.4    Magoc, T.5    Koren, S.6
  • 18
    • 0037015614 scopus 로고    scopus 로고
    • Genome sequence of the human malaria parasite Plasmodium falciparum
    • Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, et al.Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 2002; 419(6906):498-511. doi: 10.1038/nature01097.
    • (2002) Nature , vol.419 , Issue.6906 , pp. 498-511
    • Gardner, M.J.1    Hall, N.2    Fung, E.3    White, O.4    Berriman, M.5    Hyman, R.W.6
  • 19
    • 84890081976 scopus 로고    scopus 로고
    • Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM
    • arXiv.
    • Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv. 2013. doi: arXiv:1303.3997v2[q-bio.GN].
    • (2013)
    • Li, H.1
  • 21
    • 84924426384 scopus 로고    scopus 로고
    • Poretools: a toolkit for analyzing nanopore sequence data
    • Loman NJ, Quinlan AR. Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics. 2014; 30(23):3399-401. doi: 10.1093/bioinformatics/btu555.
    • (2014) Bioinformatics , vol.30 , Issue.23 , pp. 3399-3401
    • Loman, N.J.1    Quinlan, A.R.2
  • 22
    • 84952002555 scopus 로고    scopus 로고
    • Accessed 22 Apr
    • PBcR Assembler. http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR#Assembling_a_MinION_dataset. Accessed 22 Apr 2015.
    • (2015)
  • 24
    • 84857188863 scopus 로고    scopus 로고
    • Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data
    • Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics. 2012; 28(4):464-9. doi: 10.1093/bioinformatics/btr703.
    • (2012) Bioinformatics , vol.28 , Issue.4 , pp. 464-469
    • Carver, T.1    Harris, S.R.2    Berriman, M.3    Parkhill, J.4    McQuillan, J.A.5
  • 25
    • 84891822155 scopus 로고    scopus 로고
    • RefSeq microbial genomes database: new representation and annotation strategy
    • Tatusova T, Ciufo S, Fedorov B, O'Neill K, Tolstoy I. RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res. 2014; 42(D1):553-9. doi: 10.1093/nar/gkt1274.
    • (2014) Nucleic Acids Res , vol.42 , Issue.D1 , pp. 553-559
    • Tatusova, T.1    Ciufo, S.2    Fedorov, B.3    O'Neill, K.4    Tolstoy, I.5
  • 27
    • 77952299957 scopus 로고    scopus 로고
    • Prodigal: prokaryotic gene recognition and translation initiation site identification
    • Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010; 11:119. doi: 10.1186/1471-2105-11-119.
    • (2010) BMC Bioinformatics , vol.11 , pp. 119
    • Hyatt, D.1    Chen, G.L.2    Locascio, P.F.3    Land, M.L.4    Larimer, F.W.5    Hauser, L.J.6
  • 29
    • 84951945404 scopus 로고    scopus 로고
    • Accessed 22 Jun 2015.
    • PacBio circularizing and trimming. https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Circularizing-and-trimming. Accessed 22 Jun 2015.
  • 30
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAMtools
    • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al.The sequence alignment/map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. doi: 10.1093/bioinformatics/btp352.
    • (2009) Bioinformatics , vol.25 , Issue.16 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3    Fennell, T.4    Ruan, J.5    Homer, N.6
  • 31
    • 69649109364 scopus 로고    scopus 로고
    • Circos: an information aesthetic for comparative genomics
    • Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al.Circos: an information aesthetic for comparative genomics. Genome Res. 2009; 19(9):1639-45. doi: 10.1101/gr.092759.109.
    • (2009) Genome Res , vol.19 , Issue.9 , pp. 1639-1645
    • Krzywinski, M.1    Schein, J.2    Birol, I.3    Connors, J.4    Gascoyne, R.5    Horsman, D.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.