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Volumn 10, Issue 12, 2015, Pages

Evaluation and validation of assembling corrected pacbio long reads for microbial genome completion via hybrid approaches

Author keywords

[No Author keywords available]

Indexed keywords

AHA; ARTICLE; ASSEMBLING CORRECTED LONG READ; BACTERIUM; BIOINFORMATICS; CERULEAN; CONTROLLED STUDY; ECTOOL; ESCHERICHIA COLI; INFORMATION PROCESSING; LONG READ SCAFFOLDING; LORDEC; LSC; MEIOTHERMUS RUBER; MICROBIAL GENOME; NONHUMAN; PBCR PIPELINE; PDEOBACTER HEPARINUS; PROCESS DEVELOPMENT; PROOVREAD; SACCHAROMYCES CEREVISIAE; SPACE LONGREAD; VALIDATION PROCESS; ALGORITHM; DEINOCOCCUS; EVALUATION STUDY; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; PEDOBACTER; PROCEDURES; SOFTWARE; VALIDATION STUDY;

EID: 84955502827     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0144305     Document Type: Article
Times cited : (25)

References (29)
  • 1
    • 84874194145 scopus 로고    scopus 로고
    • Sequence assembly demystified
    • Epub 2013/01/30
    • Nagarajan N, Pop M. Sequence assembly demystified. Nature reviews Genetics. 2013; 14(3):157-67. Epub 2013/01/30. doi: 10.1038/nrg3367 .
    • (2013) Nature Reviews Genetics , vol.14 , Issue.3 , pp. 157-167
    • Nagarajan, N.1    Pop, M.2
  • 2
    • 84884752351 scopus 로고    scopus 로고
    • An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome
    • Ferrarini M, Moretto M, Ward JA, Surbanovski N, Stevanovic V, Giongo L, et al. An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome. BMC Genomics. 2013; 14(1):670. doi: 10.1186/1471-2164-14-670
    • (2013) BMC Genomics , vol.14 , Issue.1 , pp. 670
    • Ferrarini, M.1    Moretto, M.2    Ward, J.A.3    Surbanovski, N.4    Stevanovic, V.5    Giongo, L.6
  • 3
    • 84883664726 scopus 로고    scopus 로고
    • Reducing assembly complexity of microbial genomes with single-molecule sequencing
    • Epub 2013/09/17
    • Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM, McVey SD, et al. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biol. 2013; 14(9):R101. Epub 2013/09/17. doi: 10.1186/gb-2013-14-9-r101 .
    • (2013) Genome Biol , vol.14 , Issue.9 , pp. R101
    • Koren, S.1    Harhay, G.P.2    Smith, T.P.3    Bono, J.L.4    Harhay, D.M.5    McVey, S.D.6
  • 4
    • 84897965254 scopus 로고    scopus 로고
    • Reconstructing complex regions of genomes using long-read sequencing technology
    • Epub 2014/01/15
    • Huddleston J, Ranade S, Malig M, Antonacci F, Chaisson M, Hon L, et al. Reconstructing complex regions of genomes using long-read sequencing technology. Genome Res. 2014. Epub 2014/01/15. doi: 10.1101/gr.168450.113 .
    • (2014) Genome Res
    • Huddleston, J.1    Ranade, S.2    Malig, M.3    Antonacci, F.4    Chaisson, M.5    Hon, L.6
  • 7
    • 84868327508 scopus 로고    scopus 로고
    • Finished bacterial genomes from shotgun sequence data
    • Epub 2012/07/26
    • Ribeiro FJ, Przybylski D, Yin S, Sharpe T, Gnerre S, Abouelleil A, et al. Finished bacterial genomes from shotgun sequence data. Genome Res. 2012; 22(11):2270-7. Epub 2012/07/26. doi: 10.1101/gr. 141515.112 ; PubMed Central PMCID: PMC3483556.
    • (2012) Genome Res , vol.22 , Issue.11 , pp. 2270-2277
    • Ribeiro, F.J.1    Przybylski, D.2    Yin, S.3    Sharpe, T.4    Gnerre, S.5    Abouelleil, A.6
  • 8
    • 84880798154 scopus 로고    scopus 로고
    • Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
    • Epub 2013/05/07
    • 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. Epub 2013/05/07. 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
  • 9
    • 84884854581 scopus 로고    scopus 로고
    • Efficient and accurate whole genome assembly and methylome profiling of E. Coli
    • Powers J, Weigman V, Shu J, Pufky J, Cox D, Hurban P. Efficient and accurate whole genome assembly and methylome profiling of E. Coli. BMC Genomics. 2013; 14(1):675. doi: 10.1186/1471-2164-14-675
    • (2013) BMC Genomics , vol.14 , Issue.1 , pp. 675
    • Powers, J.1    Weigman, V.2    Shu, J.3    Pufky, J.4    Cox, D.5    Hurban, P.6
  • 10
    • 84911400440 scopus 로고    scopus 로고
    • Evaluation and validation of de novo and hybrid assembly techniques to derive high quality genome sequences
    • Utturkar SM, Klingeman DM, Land ML, Schadt CW, Doktycz MJ, Pelletier DA, et al. Evaluation and validation of de novo and hybrid assembly techniques to derive high quality genome sequences. Bioinformatics. 2014. doi: 10.1093/bioinformatics/btu391 .
    • (2014) Bioinformatics
    • Utturkar, S.M.1    Klingeman, D.M.2    Land, M.L.3    Schadt, C.W.4    Doktycz, M.J.5    Pelletier, D.A.6
  • 11
    • 84899874115 scopus 로고    scopus 로고
    • Comparison of singlemolecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia
    • Brown SD, Nagaraju S, Utturkar S, De Tissera S, Segovia S, Mitchell W, et al. Comparison of singlemolecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia. Biotechnology for biofuels. 2014; 7 (1):40. doi: 10.1186/1754-6834-7-40 .
    • (2014) Biotechnology for Biofuels , vol.7 , Issue.1 , pp. 40
    • Brown, S.D.1    Nagaraju, S.2    Utturkar, S.3    De Tissera, S.4    Segovia, S.5    Mitchell, W.6
  • 12
    • 84929993004 scopus 로고    scopus 로고
    • Completing bacterial genome assemblies: Strategy and performance comparisons
    • Liao YC, Lin SH, Lin HH. Completing bacterial genome assemblies: strategy and performance comparisons. Scientific reports. 2015; 5:8747. doi: 10.1038/srep08747 ; PubMed Central PMCID: PMC4348652.
    • (2015) Scientific Reports , vol.5 , pp. 8747
    • Liao, Y.C.1    Lin, S.H.2    Lin, H.H.3
  • 13
    • 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. Nature biotechnology. 2015; 33(6):623-30. doi: 10.1038/nbt.3238 .
    • (2015) Nature Biotechnology , 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
  • 14
    • 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. Current opinion in microbiology. 2014; 23C:110-20. doi: 10.1016/j.mib. 2014.11.014 .
    • (2014) Current Opinion in Microbiology , vol.23 , pp. 110-120
    • Koren, S.1    Phillippy, A.M.2
  • 15
    • 84955151056 scopus 로고    scopus 로고
    • Error correction and assembly complexity of single molecule sequencing reads
    • Lee H, Gurtowski J, Yoo S, Marcus S, McCombie WR, Schatz M. Error correction and assembly complexity of single molecule sequencing reads. BioRxiv. 2014. doi: 10.1101/006395
    • (2014) BioRxiv
    • Lee, H.1    Gurtowski, J.2    Yoo, S.3    Marcus, S.4    McCombie, W.R.5    Schatz, M.6
  • 16
    • 84884398663 scopus 로고    scopus 로고
    • Cerulean: A hybrid assembly using high throughput short and long reads
    • Springer
    • Deshpande V, Fung ED, Pham S, Bafna V. Cerulean: A hybrid assembly using high throughput short and long reads. Algorithms in Bioinformatics: Springer; 2013. p. 349-63.
    • (2013) Algorithms in Bioinformatics , pp. 349-363
    • Deshpande, V.1    Fung, E.D.2    Pham, S.3    Bafna, V.4
  • 17
    • 84902707563 scopus 로고    scopus 로고
    • SSPACE-LongRead: Scaffolding bacterial draft genomes using long read sequence information
    • Boetzer M, Pirovano W. SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinformatics. 2014; 15:211. doi: 10.1186/1471-2105-15-211
    • (2014) BMC Bioinformatics , vol.15 , pp. 211
    • Boetzer, M.1    Pirovano, W.2
  • 19
    • 84902509478 scopus 로고    scopus 로고
    • ExSPAnder: A universal repeat resolver for DNA fragment assembly
    • Prjibelski AD, Vasilinetc I, Bankevich A, Gurevich A, Krivosheeva T, Nurk S, et al. ExSPAnder: A universal repeat resolver for DNA fragment assembly. Bioinformatics. 2014; 30(12):i293-i301. doi: 10.1093/bioinformatics/btu266 ; PubMed Central PMCID: PMC4058921.
    • (2014) Bioinformatics , vol.30 , Issue.12 , pp. i293-i301
    • Prjibelski, A.D.1    Vasilinetc, I.2    Bankevich, A.3    Gurevich, A.4    Krivosheeva, T.5    Nurk, S.6
  • 20
    • 84913539196 scopus 로고    scopus 로고
    • LoRDEC: Accurate and efficient long read error correction
    • Salmela L, Rivals E. LoRDEC: Accurate and efficient long read error correction. Bioinformatics. 2014; 30(24):3506-14. doi: 10.1093/bioinformatics/btu538 ; PubMed Central PMCID: PMC4253826.
    • (2014) Bioinformatics , vol.30 , Issue.24 , pp. 3506-3514
    • Salmela, L.1    Rivals, E.2
  • 21
    • 84867121279 scopus 로고    scopus 로고
    • Improving PacBio long read accuracy by short read alignment
    • Epub 2012/10/12
    • Au KF, Underwood JG, Lee L, Wong WH. Improving PacBio long read accuracy by short read alignment. PLoS One. 2012; 7(10):e46679. Epub 2012/10/12. doi: 10.1371/journal.pone.0046679 ; PubMed Central PMCID: PMC3464235.
    • (2012) PLoS One , vol.7 , Issue.10 , pp. e46679
    • Au, K.F.1    Underwood, J.G.2    Lee, L.3    Wong, W.H.4
  • 22
    • 84911372793 scopus 로고    scopus 로고
    • Forster F. Proovread: Large-scale high-Accuracy PacBio correction through iterative short read consensus
    • Hackl T, Hedrich R, Schultz J, Forster F. proovread: large-scale high-Accuracy PacBio correction through iterative short read consensus. Bioinformatics. 2014; 30(21):3004-11. doi: 10.1093/bioinformatics/btu392 .
    • (2014) Bioinformatics , vol.30 , Issue.21 , pp. 3004-3011
    • Hackl, T.1    Hedrich, R.2    Schultz, J.3
  • 25
    • 84876266928 scopus 로고    scopus 로고
    • QUAST: Quality assessment tool for genome assemblies
    • Epub 2013/02/21
    • Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013; 29(8):1072-5. Epub 2013/02/21. doi: 10.1093/bioinformatics/btt086 ; PubMed Central PMCID: PMC3624806.
    • (2013) Bioinformatics , vol.29 , Issue.8 , pp. 1072-1075
    • Gurevich, A.1    Saveliev, V.2    Vyahhi, N.3    Tesler, G.4
  • 26
    • 67650711615 scopus 로고    scopus 로고
    • SOAP2: An improved ultrafast tool for short read alignment
    • Epub 2009/06/06
    • Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, et al. SOAP2: An improved ultrafast tool for short read alignment. Bioinformatics. 2009; 25(15):1966-7. Epub 2009/06/06. doi: 10.1093/bioinformatics/btp336 .
    • (2009) Bioinformatics , vol.25 , Issue.15 , pp. 1966-1967
    • Li, R.1    Yu, C.2    Li, Y.3    Lam, T.W.4    Yiu, S.M.5    Kristiansen, K.6
  • 27
    • 2942538300 scopus 로고    scopus 로고
    • Versatile and open software for comparing large genomes
    • Epub 2004/02/05
    • Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, et al. Versatile and open software for comparing large genomes. Genome Biol. 2004; 5(2):R12. Epub 2004/02/05. doi: 10.1186/gb-2004-5-2-r12 ; PubMed Central PMCID: PMC395750.
    • (2004) Genome Biol , vol.5 , Issue.2 , pp. R12
    • Kurtz, S.1    Phillippy, A.2    Delcher, A.L.3    Smoot, M.4    Shumway, M.5    Antonescu, C.6
  • 28
    • 84908635320 scopus 로고    scopus 로고
    • GABenchToB: A genome assembly benchmark tuned on bacteria and benchtop sequencers
    • Junemann S, Prior K, Albersmeier A, Albaum S, Kalinowski J, Goesmann A, et al. GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers. PLoS One. 2014; 9(9): e107014. doi: 10.1371/journal.pone.0107014 ; PubMed Central PMCID: PMC4157817.
    • (2014) PLoS One , vol.9 , Issue.9 , pp. e107014
    • Junemann, S.1    Prior, K.2    Albersmeier, A.3    Albaum, S.4    Kalinowski, J.5    Goesmann, A.6
  • 29
    • 84869814079 scopus 로고    scopus 로고
    • Mind the gap: Upgrading genomes with Pacific Biosciences RS long-read sequencing technology
    • Epub 2012/11/28
    • English AC, Richards S, Han Y, Wang M, Vee V, Qu J, et al. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One. 2012; 7(11):e47768. Epub 2012/11/28. doi: 10.1371/journal.pone.0047768 ; PubMed Central PMCID: PMC3504050.
    • (2012) PLoS One , vol.7 , Issue.11 , pp. e47768
    • English, A.C.1    Richards, S.2    Han, Y.3    Wang, M.4    Vee, V.5    Qu, J.6


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