-
1
-
-
84867121279
-
Improving PacBio long read accuracy by short read alignment
-
Au KF, Underwood JG, Lee L, Wong WH. 2012. Improving PacBio long read accuracy by short read alignment. PLoS ONE 7:e46679 DOI 10.1371/journal.pone.0046679.
-
(2012)
PLoS ONE
, vol.7
-
-
Au, K.F.1
Underwood, J.G.2
Lee, L.3
Wong, W.H.4
-
2
-
-
84930851165
-
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
-
Berlin K, Koren S, Chin C-S, Drake J, Landolin JM, Phillippy AM. 2015. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nature Biotechnology 33:623-630.
-
(2015)
Nature Biotechnology
, vol.33
, pp. 623-630
-
-
Berlin, K.1
Koren, S.2
Chin, C.-S.3
Drake, J.4
Landolin, J.M.5
Phillippy, A.M.6
-
3
-
-
84866266717
-
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory
-
Chaisson M, Tesler G. 2012. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 13:238 DOI 10.1186/1471-2105-13-238.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 238
-
-
Chaisson, M.1
Tesler, G.2
-
4
-
-
84880798154
-
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
-
Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods 10:563-569 DOI 10.1038/nmeth.2474.
-
(2013)
Nature Methods
, vol.10
, pp. 563-569
-
-
Chin, C.S.1
Alexander, D.H.2
Marks, P.3
Klammer, A.A.4
Drake, J.5
Heiner, C.6
Clum, A.7
Copeland, A.8
Huddleston, J.9
Eichler, E.E.10
Turner, S.W.11
Korlach, J.12
-
5
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792-1797 DOI 10.1093/nar/gkh340.
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
6
-
-
84911372793
-
proovread: large-scale high-accuracy PacBio correction through iterative short read consensus
-
Hackl T, Hedrich R, Schultz J, Forster F. 2014. proovread: large-scale high-accuracy PacBio correction through iterative short read consensus. Bioinformatics 30:3004-3011 DOI 10.1093/bioinformatics/btu392.
-
(2014)
Bioinformatics
, vol.30
, pp. 3004-3011
-
-
Hackl, T.1
Hedrich, R.2
Schultz, J.3
Forster, F.4
-
7
-
-
0029966581
-
Positional sequencing by hybridization
-
Hannenhalli S, Feldman W, Lewis HF, Skiena SS, Pevzner PA. 1996. Positional sequencing by hybridization. Computer Applications in the Biosciences 12:19-24.
-
(1996)
Computer Applications in the Biosciences
, vol.12
, pp. 19-24
-
-
Hannenhalli, S.1
Feldman, W.2
Lewis, H.F.3
Skiena, S.S.4
Pevzner, P.A.5
-
8
-
-
0141853948
-
PCAP: a whole-genome assembly program
-
Huang XQ, Wang JM, Aluru S, Yang SP, Hillier L. 2003. PCAP: a whole-genome assembly program. Genome Research 13:2164-2170 DOI 10.1101/gr.1390403.
-
(2003)
Genome Research
, vol.13
, pp. 2164-2170
-
-
Huang, X.Q.1
Wang, J.M.2
Aluru, S.3
Yang, S.P.4
Hillier, L.5
-
9
-
-
84863651532
-
Hybrid error correction and de novo assembly of single-molecule sequencing reads
-
Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Adam MP. 2012. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 30:693-700 DOI 10.1038/nbt.2280.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 693-700
-
-
Koren, S.1
Schatz, M.C.2
Walenz, B.P.3
Martin, J.4
Howard, J.T.5
Ganapathy, G.6
Wang, Z.7
Rasko, D.A.8
McCombie, W.R.9
Jarvis, E.D.10
Adam, M.P.11
-
10
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
Kurtz S, Phillippy A, Delcher A, Smoot M, Shumway M, Antonescu C, Salzberg S. 2004. Versatile and open software for comparing large genomes. Genome Biology 5:R12 DOI 10.1186/gb-2004-5-2-r12.
-
(2004)
Genome Biology
, vol.5
, pp. R12
-
-
Kurtz, S.1
Phillippy, A.2
Delcher, A.3
Smoot, M.4
Shumway, M.5
Antonescu, C.6
Salzberg, S.7
-
11
-
-
36448991500
-
ClustalWand clustal X version 2.0
-
Larkin MA, Blackshields G, Brown N, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R. 2007. ClustalWand clustal X version 2.0. Bioinformatics 23:2947-2948 DOI 10.1093/bioinformatics/btm404.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
-
12
-
-
84925352769
-
Assessing the performance of the Oxford Nanopore Technologies MinION
-
Laver T, Harrison J, O'Neill P, Moore K, Farbos A, Paszkiewicz K, Studholme D. 2015. Assessing the performance of the Oxford Nanopore Technologies MinION. Biomolecular Detection and Quantification 3:1-8 DOI 10.1016/j.bdq.2015.02.001.
-
(2015)
Biomolecular Detection and Quantification
, vol.3
, pp. 1-8
-
-
Laver, T.1
Harrison, J.2
O'Neill, P.3
Moore, K.4
Farbos, A.5
Paszkiewicz, K.6
Studholme, D.7
-
13
-
-
0036203448
-
Multiple sequence alignment using partial order graphs
-
Lee C, Grasso C, Sharlow MF. 2002. Multiple sequence alignment using partial order graphs. Bioinformatics 18:452-464 DOI 10.1093/bioinformatics/18.3.452.
-
(2002)
Bioinformatics
, vol.18
, pp. 452-464
-
-
Lee, C.1
Grasso, C.2
Sharlow, M.F.3
-
14
-
-
84921874530
-
-
BioRxiv Preprint. BioRxiv:006395
-
Lee H, Gurtowski J, Yoo S, Marcus S, McCombie WR, Schatz M. 2014. Error correction and assembly complexity of single molecule sequencing reads. BioRxiv Preprint. BioRxiv:006395 DOI 10.1101/006395.
-
(2014)
Error correction and assembly complexity of single molecule sequencing reads
-
-
Lee, H.1
Gurtowski, J.2
Yoo, S.3
Marcus, S.4
McCombie, W.R.5
Schatz, M.6
-
17
-
-
84958554065
-
Efficient local alignment discovery amongst noisy long reads
-
Berlin Heidelberg: Springer
-
Myers G. 2014. Efficient local alignment discovery amongst noisy long reads. In: Algorithms in bioinformatics. Berlin Heidelberg: Springer, 52-67.
-
(2014)
Algorithms in bioinformatics
, pp. 52-67
-
-
Myers, G.1
-
18
-
-
0034708758
-
A whole-genome assembly of Drosophila
-
Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM, Reinert KH, Remington KA, Anson EL, Bolanos RA, Chou HH, Jordan CM, Halpern AL, Lonardi S, Beasley EM, Brandon RC, Chen L, Dunn PJ, Lai Z, Liang Y, Nusskern DR, Zhan M, Zhang Q, Zheng X, Rubin GM, Adams MD, Venter JC. 2000. A whole-genome assembly of Drosophila. Science 287:2196-2204 DOI 10.1126/science.287.5461.2196.
-
(2000)
Science
, vol.287
, pp. 2196-2204
-
-
Myers, E.W.1
Sutton, G.G.2
Delcher, A.L.3
Dew, I.M.4
Fasulo, D.P.5
Flanigan, M.J.6
Kravitz, S.A.7
Mobarry, C.M.8
Reinert, K.H.9
Remington, K.A.10
Anson, E.L.11
Bolanos, R.A.12
Chou, H.H.13
Jordan, C.M.14
Halpern, A.L.15
Lonardi, S.16
Beasley, E.M.17
Brandon, R.C.18
Chen, L.19
Dunn, P.J.20
Lai, Z.21
Liang, Y.22
Nusskern, D.R.23
Zhan, M.24
Zhang, Q.25
Zheng, X.26
Rubin, G.M.27
Adams, M.D.28
Venter, J.C.29
more..
-
19
-
-
84874194145
-
Sequence assembly demystified
-
Nagarajan N, Pop M. 2013. Sequence assembly demystified. Nature Reviews Genetics 14:157-167 DOI 10.1038/nrg3367.
-
(2013)
Nature Reviews Genetics
, vol.14
, pp. 157-167
-
-
Nagarajan, N.1
Pop, M.2
-
21
-
-
65449134298
-
A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads
-
Rausch T, Koren S, Denisov G, Weese D, Emde AK, Doring A, Reinert K. 2009. A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinformatics 25:1118-1124 DOI 10.1093/bioinformatics/btp131.
-
(2009)
Bioinformatics
, vol.25
, pp. 1118-1124
-
-
Rausch, T.1
Koren, S.2
Denisov, G.3
Weese, D.4
Emde, A.K.5
Doring, A.6
Reinert, K.7
-
22
-
-
84863519354
-
SEQuel: improving the accuracy of genome assemblies
-
Ronen R, Boucher C, Chitsaz H, Pevzner P. 2012. SEQuel: improving the accuracy of genome assemblies. Bioinformatics 28:i188-i196 DOI 10.1093/bioinformatics/bts219.
-
(2012)
Bioinformatics
, vol.28
, pp. i188-i196
-
-
Ronen, R.1
Boucher, C.2
Chitsaz, H.3
Pevzner, P.4
-
23
-
-
84913539196
-
LoRDEC: accurate and efficient long read error correction
-
Salmela L, Rivals E. 2014. LoRDEC: accurate and efficient long read error correction. Bioinformatics 30(24):3506-3514 DOI 10.1093/bioinformatics/btu538.
-
(2014)
Bioinformatics
, vol.30
, Issue.24
, pp. 3506-3514
-
-
Salmela, L.1
Rivals, E.2
-
25
-
-
84866712746
-
Exploiting sparseness in de novo genome assembly
-
Ye C, Ma ZS, Cannon CH, Pop M, Yu DW. 2012. Exploiting sparseness in de novo genome assembly. BMC Bioinformatics 13(Suppl 6):S1 DOI 10.1186/1471-2105-13-S6-S1.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. S1
-
-
Ye, C.1
Ma, Z.S.2
Cannon, C.H.3
Pop, M.4
Yu, D.W.5
|