-
1
-
-
79959212998
-
Landscape of next-generation sequencing technologies
-
Niedringhaus TP, Milanova D, Kerby MB, Snyder MP, Barron AE, (2011) Landscape of next-generation sequencing technologies. Anal Chem 83: 4327-4341.
-
(2011)
Anal Chem
, vol.83
, pp. 4327-4341
-
-
Niedringhaus, T.P.1
Milanova, D.2
Kerby, M.B.3
Snyder, M.P.4
Barron, A.E.5
-
2
-
-
64149123778
-
Next-generation sequencing: from basic research to diagnostics
-
Voelkerding KV, Dames SA, Durtschi JD, (2009) Next-generation sequencing: from basic research to diagnostics. Clin Chem 55: 641-658.
-
(2009)
Clin Chem
, vol.55
, pp. 641-658
-
-
Voelkerding, K.V.1
Dames, S.A.2
Durtschi, J.D.3
-
3
-
-
84864302486
-
Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics
-
Helmy M, Sugiyama N, Tomita M, Ishihama Y, (2012) Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics. Genes Cells 17: 633-644.
-
(2012)
Genes Cells
, vol.17
, pp. 633-644
-
-
Helmy, M.1
Sugiyama, N.2
Tomita, M.3
Ishihama, Y.4
-
4
-
-
84864317940
-
Peptide identification by searching large-scale tandem mass spectra against large databases: bioinformatics methods in proteogenomics
-
Helmy M, Tomita M, Ishihama Y, (2011) Peptide identification by searching large-scale tandem mass spectra against large databases: bioinformatics methods in proteogenomics. Genes, Genomes and Genomics 6: 76-85.
-
(2011)
Genes, Genomes and Genomics
, vol.6
, pp. 76-85
-
-
Helmy, M.1
Tomita, M.2
Ishihama, Y.3
-
5
-
-
79953167500
-
The next-generation sequencing technology and application
-
Zhou X, Ren L, Meng Q, Li Y, Yu Y, et al. (2010) The next-generation sequencing technology and application. Protein Cell 1: 520-536.
-
(2010)
Protein Cell
, vol.1
, pp. 520-536
-
-
Zhou, X.1
Ren, L.2
Meng, Q.3
Li, Y.4
Yu, Y.5
-
6
-
-
84864920004
-
Comparison of next-generation sequencing systems
-
Liu L, Li Y, Li S, Hu N, He Y, et al. (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012: 251364.
-
(2012)
J Biomed Biotechnol
, vol.2012
, pp. 251364
-
-
Liu, L.1
Li, Y.2
Li, S.3
Hu, N.4
He, Y.5
-
7
-
-
43149086380
-
ALLPATHS: de novo assembly of whole-genome shotgun microreads
-
Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, et al. (2008) ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 18: 810-820.
-
(2008)
Genome Res
, vol.18
, pp. 810-820
-
-
Butler, J.1
MacCallum, I.2
Kleber, M.3
Shlyakhter, I.A.4
Belmonte, M.K.5
-
9
-
-
59949093527
-
De novo fragment assembly with short mate-paired reads: does the read length matter?
-
Chaisson MJ, Brinza D, Pevzner PA, (2009) De novo fragment assembly with short mate-paired reads: does the read length matter? Genome Res 19: 336-346.
-
(2009)
Genome Res
, vol.19
, pp. 336-346
-
-
Chaisson, M.J.1
Brinza, D.2
Pevzner, P.A.3
-
10
-
-
39049156065
-
Short read fragment assembly of bacterial genomes
-
Chaisson MJ, Pevzner PA, (2008) Short read fragment assembly of bacterial genomes. Genome Res 18: 324-330.
-
(2008)
Genome Res
, vol.18
, pp. 324-330
-
-
Chaisson, M.J.1
Pevzner, P.A.2
-
11
-
-
76249102138
-
De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data
-
DiGuistini S, Liao NY, Platt D, Robertson G, Seidel M, et al. (2009) De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biol 10: R94.
-
(2009)
Genome Biol
, vol.10
-
-
DiGuistini, S.1
Liao, N.Y.2
Platt, D.3
Robertson, G.4
Seidel, M.5
-
12
-
-
35948929094
-
SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing
-
Dohm JC, Lottaz C, Borodina T, Himmelbauer H, (2007) SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res 17: 1697-1706.
-
(2007)
Genome Res
, vol.17
, pp. 1697-1706
-
-
Dohm, J.C.1
Lottaz, C.2
Borodina, T.3
Himmelbauer, H.4
-
13
-
-
84860523681
-
Readjoiner: a fast and memory efficient string graph-based sequence assembler
-
Gonnella G, Kurtz S, (2012) Readjoiner: a fast and memory efficient string graph-based sequence assembler. BMC Bioinformatics 13: 82.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 82
-
-
Gonnella, G.1
Kurtz, S.2
-
14
-
-
43149085041
-
De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer
-
Hernandez D, Francois P, Farinelli L, Osteras M, Schrenzel J, (2008) De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res 18: 802-809.
-
(2008)
Genome Res
, vol.18
, pp. 802-809
-
-
Hernandez, D.1
Francois, P.2
Farinelli, L.3
Osteras, M.4
Schrenzel, J.5
-
16
-
-
84863651532
-
Hybrid error correction and de novo assembly of single-molecule sequencing reads
-
Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, et al. (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 30: 693-700.
-
(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
-
17
-
-
75649124547
-
De novo assembly of human genomes with massively parallel short read sequencing
-
Li R, Zhu H, Ruan J, Qian W, Fang X, et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20: 265-272.
-
(2010)
Genome Res
, vol.20
, pp. 265-272
-
-
Li, R.1
Zhu, H.2
Ruan, J.3
Qian, W.4
Fang, X.5
-
18
-
-
75349109607
-
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
-
Maccallum I, Przybylski D, Gnerre S, Burton J, Shlyakhter I, et al. (2009) ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol 10: R103.
-
(2009)
Genome Biol
, vol.10
-
-
Maccallum, I.1
Przybylski, D.2
Gnerre, S.3
Burton, J.4
Shlyakhter, I.5
-
19
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
-
20
-
-
80052960863
-
Next-generation transcriptome assembly
-
Martin JA, Wang Z, (2011) Next-generation transcriptome assembly. Nat Rev Genet 12: 671-682.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 671-682
-
-
Martin, J.A.1
Wang, Z.2
-
21
-
-
57249105124
-
Aggressive assembly of pyrosequencing reads with mates
-
Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, et al. (2008) Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24: 2818-2824.
-
(2008)
Bioinformatics
, vol.24
, pp. 2818-2824
-
-
Miller, J.R.1
Delcher, A.L.2
Koren, S.3
Venter, E.4
Walenz, B.P.5
-
22
-
-
77952886150
-
Assembly algorithms for next-generation sequencing data
-
Miller JR, Koren S, Sutton G, (2010) Assembly algorithms for next-generation sequencing data. Genomics 95: 315-327.
-
(2010)
Genomics
, vol.95
, pp. 315-327
-
-
Miller, J.R.1
Koren, S.2
Sutton, G.3
-
23
-
-
0034708758
-
A whole-genome assembly of Drosophila
-
Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, et al. (2000) A whole-genome assembly of Drosophila. Science 287: 2196-2204.
-
(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
-
24
-
-
84874194145
-
Sequence assembly demystified
-
Nagarajan N, Pop M, (2013) Sequence assembly demystified. Nat Rev Genet 14: 157-167.
-
(2013)
Nat Rev Genet
, vol.14
, pp. 157-167
-
-
Nagarajan, N.1
Pop, M.2
-
25
-
-
77957287342
-
De novo assembly of short sequence reads
-
Paszkiewicz K, Studholme DJ, (2010) De novo assembly of short sequence reads. Brief Bioinform 11: 457-472.
-
(2010)
Brief Bioinform
, vol.11
, pp. 457-472
-
-
Paszkiewicz, K.1
Studholme, D.J.2
-
26
-
-
0035232164
-
Fragment assembly with double-barreled data
-
Pevzner PA, Tang H, (2001) Fragment assembly with double-barreled data. Bioinformatics 17 (Suppl 1) (): S225-233.
-
(2001)
Bioinformatics
, vol.17
, Issue.SUPPL. 1
-
-
Pevzner, P.A.1
Tang, H.2
-
28
-
-
59949090259
-
De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
-
Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, et al. (2009) De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res 19: 294-305.
-
(2009)
Genome Res
, vol.19
, pp. 294-305
-
-
Reinhardt, J.A.1
Baltrus, D.A.2
Nishimura, M.T.3
Jeck, W.R.4
Jones, C.D.5
-
29
-
-
69949167273
-
A fast hybrid short read fragment assembly algorithm
-
Schmidt B, Sinha R, Beresford-Smith B, Puglisi SJ, (2009) A fast hybrid short read fragment assembly algorithm. Bioinformatics 25: 2279-2280.
-
(2009)
Bioinformatics
, vol.25
, pp. 2279-2280
-
-
Schmidt, B.1
Sinha, R.2
Beresford-Smith, B.3
Puglisi, S.J.4
-
30
-
-
84857838310
-
Efficient de novo assembly of large genomes using compressed data structures
-
Simpson JT, Durbin R, (2012) Efficient de novo assembly of large genomes using compressed data structures. Genome Res 22: 549-556.
-
(2012)
Genome Res
, vol.22
, pp. 549-556
-
-
Simpson, J.T.1
Durbin, R.2
-
31
-
-
66449136667
-
ABySS: a parallel assembler for short read sequence data
-
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19: 1117-1123.
-
(2009)
Genome Res
, vol.19
, pp. 1117-1123
-
-
Simpson, J.T.1
Wong, K.2
Jackman, S.D.3
Schein, J.E.4
Jones, S.J.5
-
32
-
-
84878820440
-
Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome
-
Wang Y, Yu Y, Pan B, Hao P, Li Y, et al. (2012) Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome. BMC Syst Biol 6: 1-13.
-
(2012)
BMC Syst Biol
, vol.6
, pp. 1-13
-
-
Wang, Y.1
Yu, Y.2
Pan, B.3
Hao, P.4
Li, Y.5
-
33
-
-
33847307402
-
Assembling millions of short DNA sequences using SSAKE
-
Warren RL, Sutton GG, Jones SJM, Holt RA, (2006) Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23: 500-501.
-
(2006)
Bioinformatics
, vol.23
, pp. 500-501
-
-
Warren, R.L.1
Sutton, G.G.2
Jones, S.J.M.3
Holt, R.A.4
-
34
-
-
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.
-
(2012)
BMC Bioinformatics
, vol.13
, Issue.SUPPL. 6
-
-
Ye, C.1
Ma, Z.S.2
Cannon, C.H.3
Pop, M.4
Yu, D.W.5
-
35
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino DR, Birney E, (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
36
-
-
84865591846
-
A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
-
Quail MA, Smith M, Coupland P, Otto TD, Harris SR, et al. (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13: 341.
-
(2012)
BMC Genomics
, vol.13
, pp. 341
-
-
Quail, M.A.1
Smith, M.2
Coupland, P.3
Otto, T.D.4
Harris, S.R.5
-
37
-
-
83255173973
-
Short reads, circular genome: skimming solid sequence to construct the bighorn sheep mitochondrial genome
-
Miller JM, Malenfant RM, Moore SS, Coltman DW, (2012) Short reads, circular genome: skimming solid sequence to construct the bighorn sheep mitochondrial genome. J Hered 103: 140-146.
-
(2012)
J Hered
, vol.103
, pp. 140-146
-
-
Miller, J.M.1
Malenfant, R.M.2
Moore, S.S.3
Coltman, D.W.4
-
38
-
-
84860756398
-
Performance comparison of benchtop high-throughput sequencing platforms
-
Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, et al. (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30: 434-439.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 434-439
-
-
Loman, N.J.1
Misra, R.V.2
Dallman, T.J.3
Constantinidou, C.4
Gharbia, S.E.5
-
39
-
-
84865992574
-
A survey of error-correction methods for next-generation sequencing
-
Yang X, Chockalingam SP, Aluru S, (2013) A survey of error-correction methods for next-generation sequencing. Brief Bioinform 14: 56-66.
-
(2013)
Brief Bioinform
, vol.14
, pp. 56-66
-
-
Yang, X.1
Chockalingam, S.P.2
Aluru, S.3
-
40
-
-
84892710108
-
-
Sequence Read Archive. Available:. Accessed 4 February
-
Sequence Read Archive. Available: http://www.ncbi.nlm.nih.gov/sra. Accessed 4 February 2013.
-
(2013)
-
-
-
41
-
-
84892768273
-
-
Assembly Archive. Available:. Accessed 4 February
-
Assembly Archive. Available: http://www.ncbi.nlm.nih.gov/Traces/assembly/. Accessed 4 February 2013.
-
(2013)
-
-
-
42
-
-
84892693378
-
-
AGP file. Available:. Accessed 4 February
-
AGP file. Available: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/agp/. Accessed 4 February 2013.
-
(2013)
-
-
-
43
-
-
16644381328
-
Comparative genome assembly
-
Pop M, Phillippy A, Delcher AL, Salzberg SL, (2004) Comparative genome assembly. Brief Bioinform 5: 237-248.
-
(2004)
Brief Bioinform
, vol.5
, pp. 237-248
-
-
Pop, M.1
Phillippy, A.2
Delcher, A.L.3
Salzberg, S.L.4
-
44
-
-
79952655567
-
A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies
-
doi:10.1371/journal.pone.0017915
-
Zhang W, Chen J, Yang Y, Tang Y, Shang J, et al. (2011) A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies. PLoS ONE 6: e17915 doi:10.1371/journal.pone.0017915.
-
(2011)
PLoS ONE
, vol.6
-
-
Zhang, W.1
Chen, J.2
Yang, Y.3
Tang, Y.4
Shang, J.5
-
45
-
-
79551589417
-
HiTEC: accurate error correction in high-throughput sequencing data
-
Ilie L, Fazayeli F, Ilie S, (2011) HiTEC: accurate error correction in high-throughput sequencing data. Bioinformatics 27: 295-302.
-
(2011)
Bioinformatics
, vol.27
, pp. 295-302
-
-
Ilie, L.1
Fazayeli, F.2
Ilie, S.3
-
46
-
-
79959867627
-
ECHO: a reference-free short-read error correction algorithm
-
Kao WC, Chan AH, Song YS, (2011) ECHO: a reference-free short-read error correction algorithm. Genome Res 21: 1181-1192.
-
(2011)
Genome Res
, vol.21
, pp. 1181-1192
-
-
Kao, W.C.1
Chan, A.H.2
Song, Y.S.3
-
47
-
-
78649358717
-
Quake: quality-aware detection and correction of sequencing errors
-
Kelley DR, Schatz MC, Salzberg SL, (2010) Quake: quality-aware detection and correction of sequencing errors. Genome Biol 11: R116.
-
(2010)
Genome Biol
, vol.11
-
-
Kelley, D.R.1
Schatz, M.C.2
Salzberg, S.L.3
-
48
-
-
79959485321
-
Error correction of high-throughput sequencing datasets with non-uniform coverage
-
Medvedev P, Scott E, Kakaradov B, Pevzner P, (2011) Error correction of high-throughput sequencing datasets with non-uniform coverage. Bioinformatics 27: i137-i141.
-
(2011)
Bioinformatics
, vol.27
-
-
Medvedev, P.1
Scott, E.2
Kakaradov, B.3
Pevzner, P.4
-
49
-
-
79957814500
-
Correcting errors in short reads by multiple alignments
-
Salmela L, Schroder J, (2011) Correcting errors in short reads by multiple alignments. Bioinformatics 27: 1455-1461.
-
(2011)
Bioinformatics
, vol.27
, pp. 1455-1461
-
-
Salmela, L.1
Schroder, J.2
-
50
-
-
69949178009
-
SHREC: a short-read error correction method
-
Schroder J, Schroder H, Puglisi SJ, Sinha R, Schmidt B, (2009) SHREC: a short-read error correction method. Bioinformatics 25: 2157-2163.
-
(2009)
Bioinformatics
, vol.25
, pp. 2157-2163
-
-
Schroder, J.1
Schroder, H.2
Puglisi, S.J.3
Sinha, R.4
Schmidt, B.5
-
51
-
-
77957758142
-
Reptile: representative tiling for short read error correction
-
Yang X, Dorman KS, Aluru S, (2010) Reptile: representative tiling for short read error correction. Bioinformatics 26: 2526-2533.
-
(2010)
Bioinformatics
, vol.26
, pp. 2526-2533
-
-
Yang, X.1
Dorman, K.S.2
Aluru, S.3
-
52
-
-
79951530130
-
Scaffolding pre-assembled contigs using SSPACE
-
Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W, (2011) Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 24: 578-579.
-
(2011)
Bioinformatics
, vol.24
, pp. 578-579
-
-
Boetzer, M.1
Henkel, C.V.2
Jansen, H.J.3
Butler, D.4
Pirovano, W.5
-
53
-
-
77954324418
-
SOPRA: scaffolding algorithm for paired reads via statistical optimization
-
Dayarian A, Michael TP, Sengupta AM, (2010) SOPRA: scaffolding algorithm for paired reads via statistical optimization. BMC Bioinformatics 11: 345.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 345
-
-
Dayarian, A.1
Michael, T.P.2
Sengupta, A.M.3
-
54
-
-
84874330144
-
SCARPA: scaffolding reads with practical algorithms
-
Donmez N, Brudno M, (2013) SCARPA: scaffolding reads with practical algorithms. Bioinformatics 29: 428-434.
-
(2013)
Bioinformatics
, vol.29
, pp. 428-434
-
-
Donmez, N.1
Brudno, M.2
-
55
-
-
80955159932
-
Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences
-
Gao S, Sung WK, Nagarajan N, (2011) Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. J Comput Biol 18: 1681-1691.
-
(2011)
J Comput Biol
, vol.18
, pp. 1681-1691
-
-
Gao, S.1
Sung, W.K.2
Nagarajan, N.3
-
57
-
-
82255185486
-
Fast scaffolding with small independent mixed integer programs
-
Salmela L, Makinen V, Valimaki N, Ylinen J, Ukkonen E, (2011) Fast scaffolding with small independent mixed integer programs. Bioinformatics 27: 3259-3265.
-
(2011)
Bioinformatics
, vol.27
, pp. 3259-3265
-
-
Salmela, L.1
Makinen, V.2
Valimaki, N.3
Ylinen, J.4
Ukkonen, E.5
-
58
-
-
84863181401
-
Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph
-
Li Z, Chen Y, Mu D, Yuan J, Shi Y, et al. (2012) Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph. Brief Funct Genomics 11: 25-37.
-
(2012)
Brief Funct Genomics
, vol.11
, pp. 25-37
-
-
Li, Z.1
Chen, Y.2
Mu, D.3
Yuan, J.4
Shi, Y.5
-
59
-
-
79952178131
-
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
-
Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, et al. (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A 108: 1513-1518.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 1513-1518
-
-
Gnerre, S.1
Maccallum, I.2
Przybylski, D.3
Ribeiro, F.J.4
Burton, J.N.5
-
60
-
-
84864119729
-
Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly
-
Li H, (2012) Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics 28: 1838-1844.
-
(2012)
Bioinformatics
, vol.28
, pp. 1838-1844
-
-
Li, H.1
-
61
-
-
79952108717
-
Sequencing and genome assembly using next-generation technologies
-
In: Fenyö D, editor. Humana Press
-
Nagarajan N, Pop M (2010) Sequencing and genome assembly using next-generation technologies. In: Fenyö D, editor. Computational biology. Humana Press. pp. 1-17.
-
(2010)
Computational biology
, pp. 1-17
-
-
Nagarajan, N.1
Pop, M.2
-
62
-
-
77952857079
-
Correction of sequencing errors in a mixed set of reads
-
Salmela L, (2010) Correction of sequencing errors in a mixed set of reads. Bioinformatics 26: 1284-1290.
-
(2010)
Bioinformatics
, vol.26
, pp. 1284-1290
-
-
Salmela, L.1
-
63
-
-
84857893016
-
GAGE: a critical evaluation of genome assemblies and assembly algorithms
-
Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, et al. (2012) GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res 22: 557-567.
-
(2012)
Genome Res
, vol.22
, pp. 557-567
-
-
Salzberg, S.L.1
Phillippy, A.M.2
Zimin, A.3
Puiu, D.4
Magoc, T.5
-
64
-
-
70349204183
-
Maximum likelihood genome assembly
-
Medvedev P, Brudno M, (2009) Maximum likelihood genome assembly. J Comput Biol 16: 1101-1116.
-
(2009)
J Comput Biol
, vol.16
, pp. 1101-1116
-
-
Medvedev, P.1
Brudno, M.2
-
65
-
-
37249080658
-
Computability of models for sequence assembly
-
In: Giancarlo R, Hannenhalli S, editors. Springer Berlin Heidelberg
-
Medvedev P, Georgiou K, Myers G, Brudno M (2007) Computability of models for sequence assembly. In: Giancarlo R, Hannenhalli S, editors. Algorithms in bioinformatics. Springer Berlin Heidelberg. pp. 289-301.
-
(2007)
Algorithms in bioinformatics
, pp. 289-301
-
-
Medvedev, P.1
Georgiou, K.2
Myers, G.3
Brudno, M.4
-
66
-
-
0021760072
-
SEQAID: a DNA sequence assembling program based on a mathematical model
-
Peltola H, Soderlund H, Ukkonen E, (1984) SEQAID: a DNA sequence assembling program based on a mathematical model. Nucleic Acids Res 12: 307-321.
-
(1984)
Nucleic Acids Res
, vol.12
, pp. 307-321
-
-
Peltola, H.1
Soderlund, H.2
Ukkonen, E.3
-
67
-
-
27544497879
-
The fragment assembly string graph
-
Myers EW, (2005) The fragment assembly string graph. Bioinformatics 21 (Suppl 2) (): ii79-85.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 2
-
-
Myers, E.W.1
-
68
-
-
77954238055
-
Efficient construction of an assembly string graph using the FM-index
-
Simpson JT, Durbin R, (2010) Efficient construction of an assembly string graph using the FM-index. Bioinformatics 26: i367-373.
-
(2010)
Bioinformatics
, vol.26
-
-
Simpson, J.T.1
Durbin, R.2
-
69
-
-
0029312687
-
A new algorithm for DNA sequence assembly
-
Idury RM, Waterman MS, (1995) A new algorithm for DNA sequence assembly. J Comput Biol 2: 291-306.
-
(1995)
J Comput Biol
, vol.2
, pp. 291-306
-
-
Idury, R.M.1
Waterman, M.S.2
-
70
-
-
79960872039
-
Evaluation of short read metagenomic assembly
-
Charuvaka A, Rangwala H, (2011) Evaluation of short read metagenomic assembly. BMC Genomics 12 (Suppl 2) (): S8.
-
(2011)
BMC Genomics
, vol.12
, Issue.SUPPL. 2
-
-
Charuvaka, A.1
Rangwala, H.2
-
71
-
-
81155158421
-
Efficient counting of k-mers in DNA sequences using a bloom filter
-
Melsted P, Pritchard J, (2011) Efficient counting of k-mers in DNA sequences using a bloom filter. BMC Bioinformatics 12: 1-7.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 1-7
-
-
Melsted, P.1
Pritchard, J.2
-
72
-
-
79951526698
-
Succinct data structures for assembling large genomes
-
Conway TC, Bromage AJ, (2011) Succinct data structures for assembling large genomes. Bioinformatics 27: 479-486.
-
(2011)
Bioinformatics
, vol.27
, pp. 479-486
-
-
Conway, T.C.1
Bromage, A.J.2
-
73
-
-
84866656074
-
Succinct de Bruijn Graphs
-
In: Raphael B, Tang J, editors. Springer Berlin Heidelberg
-
Bowe A, Onodera T, Sadakane K, Shibuya T (2012) Succinct de Bruijn Graphs. In: Raphael B, Tang J, editors. Algorithms in bioinformatics. Springer Berlin Heidelberg. pp. 225-235.
-
(2012)
Algorithms in bioinformatics
, pp. 225-235
-
-
Bowe, A.1
Onodera, T.2
Sadakane, K.3
Shibuya, T.4
-
74
-
-
36448948250
-
Extending assembly of short DNA sequences to handle error
-
Jeck WR, Reinhardt JA, Baltrus DA, Hickenbotham MT, Magrini V, et al. (2007) Extending assembly of short DNA sequences to handle error. Bioinformatics 23: 2942-2944.
-
(2007)
Bioinformatics
, vol.23
, pp. 2942-2944
-
-
Jeck, W.R.1
Reinhardt, J.A.2
Baltrus, D.A.3
Hickenbotham, M.T.4
Magrini, V.5
-
76
-
-
58349105386
-
High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies
-
Aury J-M, Cruaud C, Barbe V, Rogier O, Mangenot S, et al. (2008) High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies. BMC Genomics 9: 1-11.
-
(2008)
BMC Genomics
, vol.9
, pp. 1-11
-
-
Aury, J.-M.1
Cruaud, C.2
Barbe, V.3
Rogier, O.4
Mangenot, S.5
-
77
-
-
79959723260
-
Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study
-
Cerdeira LT, Carneiro AR, Ramos RTJ, de Almeida SS, D'Afonseca V, et al. (2011) Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study. J Microbiol Methods 86: 218-223.
-
(2011)
J Microbiol Methods
, vol.86
, pp. 218-223
-
-
Cerdeira, L.T.1
Carneiro, A.R.2
Ramos, R.T.J.3
de Almeida, S.S.4
D'Afonseca, V.5
-
78
-
-
77956532052
-
Integrating genome assemblies with MAIA
-
Nijkamp J, Winterbach W, van den Broek M, Daran JM, Reinders M, et al. (2010) Integrating genome assemblies with MAIA. Bioinformatics 26: i433-439.
-
(2010)
Bioinformatics
, vol.26
-
-
Nijkamp, J.1
Winterbach, W.2
van den Broek, M.3
Daran, J.M.4
Reinders, M.5
-
79
-
-
77949511368
-
Pebble and Rock Band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler
-
doi:10.1371/journal.pone.0008407
-
Zerbino DR, McEwen GK, Margulies EH, Birney E, (2009) Pebble and Rock Band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. PLoS ONE 4: e8407 doi:10.1371/journal.pone.0008407.
-
(2009)
PLoS ONE
, vol.4
-
-
Zerbino, D.R.1
McEwen, G.K.2
Margulies, E.H.3
Birney, E.4
-
81
-
-
1242281253
-
The greedy path-merging algorithm for contig scaffolding
-
Huson DH, Reinert K, Myers EW, (2002) The greedy path-merging algorithm for contig scaffolding. Journal of the ACM 49: 603-615.
-
(2002)
Journal of the ACM
, vol.49
, pp. 603-615
-
-
Huson, D.H.1
Reinert, K.2
Myers, E.W.3
-
82
-
-
80955139667
-
Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers
-
Medvedev P, Pham S, Chaisson M, Tesler G, Pevzner P, (2011) Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. J Comput Biol 18: 1625-1634.
-
(2011)
J Comput Biol
, vol.18
, pp. 1625-1634
-
-
Medvedev, P.1
Pham, S.2
Chaisson, M.3
Tesler, G.4
Pevzner, P.5
-
84
-
-
78650909427
-
Limitations of next-generation genome sequence assembly
-
Alkan C, Sajjadian S, Eichler EE, (2011) Limitations of next-generation genome sequence assembly. Nat Methods 8: 61-65.
-
(2011)
Nat Methods
, vol.8
, pp. 61-65
-
-
Alkan, C.1
Sajjadian, S.2
Eichler, E.E.3
-
85
-
-
84870007007
-
Slim-Filter: an interactive windows-based application for illumina genome analyzer data assessment and manipulation
-
Golovko G, Khanipov K, Rojas M, Martinez-Alcantara A, Howard JJ, et al. (2012) Slim-Filter: an interactive windows-based application for illumina genome analyzer data assessment and manipulation. BMC Bioinformatics 13: 166.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 166
-
-
Golovko, G.1
Khanipov, K.2
Rojas, M.3
Martinez-Alcantara, A.4
Howard, J.J.5
-
86
-
-
84872557118
-
VAGUE: a graphical user interface for the Velvet assembler
-
Powell DR, Seemann T, (2013) VAGUE: a graphical user interface for the Velvet assembler. Bioinformatics 29: 264-265.
-
(2013)
Bioinformatics
, vol.29
, pp. 264-265
-
-
Powell, D.R.1
Seemann, T.2
-
87
-
-
66249148986
-
Lineage-specific biology revealed by a finished genome assembly of the mouse
-
doi:10.1371/journal.pbio.1000112
-
Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, et al. (2009) Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol 7: e1000112 doi:10.1371/journal.pbio.1000112.
-
(2009)
PLoS Biol
, vol.7
-
-
Church, D.M.1
Goodstadt, L.2
Hillier, L.W.3
Zody, M.C.4
Goldstein, S.5
-
88
-
-
79551632781
-
The ecoresponsive genome of Daphnia pulex
-
Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, et al. (2011) The ecoresponsive genome of Daphnia pulex. Science 331: 555-561.
-
(2011)
Science
, vol.331
, pp. 555-561
-
-
Colbourne, J.K.1
Pfrender, M.E.2
Gilbert, D.3
Thomas, W.K.4
Tucker, A.5
-
89
-
-
75149155568
-
The sequence and de novo assembly of the giant panda genome
-
Li R, Fan W, Tian G, Zhu H, He L, et al. (2010) The sequence and de novo assembly of the giant panda genome. Nature 463: 311-317.
-
(2010)
Nature
, vol.463
, pp. 311-317
-
-
Li, R.1
Fan, W.2
Tian, G.3
Zhu, H.4
He, L.5
-
90
-
-
28644447707
-
Genome sequence, comparative analysis and haplotype structure of the domestic dog
-
Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, et al. (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438: 803-819.
-
(2005)
Nature
, vol.438
, pp. 803-819
-
-
Lindblad-Toh, K.1
Wade, C.M.2
Mikkelsen, T.S.3
Karlsson, E.K.4
Jaffe, D.B.5
-
91
-
-
65449187055
-
Bos taurus genome assembly
-
Liu Y, Qin X, Song XZ, Jiang H, Shen Y, et al. (2009) Bos taurus genome assembly. BMC Genomics 10: 180.
-
(2009)
BMC Genomics
, vol.10
, pp. 180
-
-
Liu, Y.1
Qin, X.2
Song, X.Z.3
Jiang, H.4
Shen, Y.5
-
92
-
-
79251553493
-
Comparative and demographic analysis of orang-utan genomes
-
Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, et al. (2011) Comparative and demographic analysis of orang-utan genomes. Nature 469: 529-533.
-
(2011)
Nature
, vol.469
, pp. 529-533
-
-
Locke, D.P.1
Hillier, L.W.2
Warren, W.C.3
Worley, K.C.4
Nazareth, L.V.5
-
93
-
-
42949157236
-
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
-
Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, et al. (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452: 991-996.
-
(2008)
Nature
, vol.452
, pp. 991-996
-
-
Ming, R.1
Hou, S.2
Feng, Y.3
Yu, Q.4
Dionne-Laporte, A.5
-
94
-
-
79960411408
-
Comparative studies of de novo assembly tools for next-generation sequencing technologies
-
Lin Y, Li J, Shen H, Zhang L, Papasian CJ, et al. (2011) Comparative studies of de novo assembly tools for next-generation sequencing technologies. Bioinformatics 27: 2031-2037.
-
(2011)
Bioinformatics
, vol.27
, pp. 2031-2037
-
-
Lin, Y.1
Li, J.2
Shen, H.3
Zhang, L.4
Papasian, C.J.5
-
95
-
-
84959064984
-
-
A°rhus, Denmark: Springer Berlin Heidelberg
-
Huson DH, Halpern AL, Lai Z, Myers EW, Reinert K, et al. (2001) Comparing assemblies using fragments and mate-pairs. Århus, Denmark: Springer Berlin Heidelberg. pp. 294-306.
-
(2001)
Comparing assemblies using fragments and mate-pairs
, pp. 294-306
-
-
Huson, D.H.1
Halpern, A.L.2
Lai, Z.3
Myers, E.W.4
Reinert, K.5
-
96
-
-
45549109750
-
Genome assembly forensics: finding the elusive mis-assembly
-
Phillippy AM, Schatz MC, Pop M, (2008) Genome assembly forensics: finding the elusive mis-assembly. Genome Biol 9: R55.
-
(2008)
Genome Biol
, vol.9
-
-
Phillippy, A.M.1
Schatz, M.C.2
Pop, M.3
-
97
-
-
35649003378
-
Validation of rice genome sequence by optical mapping
-
Zhou S, Bechner MC, Place M, Churas CP, Pape L, et al. (2007) Validation of rice genome sequence by optical mapping. BMC Genomics 8: 278.
-
(2007)
BMC Genomics
, vol.8
, pp. 278
-
-
Zhou, S.1
Bechner, M.C.2
Place, M.3
Churas, C.P.4
Pape, L.5
-
98
-
-
58549121169
-
Assessing the gene space in draft genomes
-
Parra G, Bradnam K, Ning Z, Keane T, Korf I, (2009) Assessing the gene space in draft genomes. Nucleic Acids Res 37: 289-297.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 289-297
-
-
Parra, G.1
Bradnam, K.2
Ning, Z.3
Keane, T.4
Korf, I.5
-
99
-
-
79952065370
-
Error and error mitigation in low-coverage genome assemblies
-
doi:10.1371/journal.pone.0017034
-
Hubisz MJ, Lin MF, Kellis M, Siepel A, (2011) Error and error mitigation in low-coverage genome assemblies. PLoS ONE 6: e17034 doi:10.1371/journal.pone.0017034.
-
(2011)
PLoS ONE
, vol.6
-
-
Hubisz, M.J.1
Lin, M.F.2
Kellis, M.3
Siepel, A.4
-
100
-
-
77951813504
-
Genome assembly quality: assessment and improvement using the neutral indel model
-
Meader S, Hillier LW, Locke D, Ponting CP, Lunter G, (2010) Genome assembly quality: assessment and improvement using the neutral indel model. Genome Res 20: 675-684.
-
(2010)
Genome Res
, vol.20
, pp. 675-684
-
-
Meader, S.1
Hillier, L.W.2
Locke, D.3
Ponting, C.P.4
Lunter, G.5
-
101
-
-
83055181941
-
Assemblathon 1: a competitive assessment of de novo short read assembly methods
-
Earl D, Bradnam K, St John J, Darling A, Lin D, et al. (2011) Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res 21: 2224-2241.
-
(2011)
Genome Res
, vol.21
, pp. 2224-2241
-
-
Earl, D.1
Bradnam, K.2
St John, J.3
Darling, A.4
Lin, D.5
-
102
-
-
80052530006
-
Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results
-
doi:10.1371/journal.pone.0024182
-
Haiminen N, Kuhn DN, Parida L, Rigoutsos I, (2011) Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results. PLoS ONE 6: e24182 doi:10.1371/journal.pone.0024182.
-
(2011)
PLoS ONE
, vol.6
-
-
Haiminen, N.1
Kuhn, D.N.2
Parida, L.3
Rigoutsos, I.4
-
103
-
-
79955724657
-
Comparing de novo genome assembly: the long and short of it
-
doi:10.1371/journal.pone.0019175
-
Narzisi G, Mishra B, (2011) Comparing de novo genome assembly: the long and short of it. PLoS ONE 6: e19175 doi:10.1371/journal.pone.0019175.
-
(2011)
PLoS ONE
, vol.6
-
-
Narzisi, G.1
Mishra, B.2
-
104
-
-
84856557873
-
Feature-by-feature - evaluating de novo sequence assembly
-
doi:10.1371/journal.pone.0031002
-
Vezzi F, Narzisi G, Mishra B, (2012) Feature-by-feature - evaluating de novo sequence assembly. PLoS ONE 7: e31002 doi:10.1371/journal.pone.0031002.
-
(2012)
PLoS ONE
, vol.7
-
-
Vezzi, F.1
Narzisi, G.2
Mishra, B.3
-
105
-
-
67449095888
-
Genome assembly reborn: recent computational challenges
-
Pop M, (2009) Genome assembly reborn: recent computational challenges. Brief Bioinform 10: 354-366.
-
(2009)
Brief Bioinform
, vol.10
, pp. 354-366
-
-
Pop, M.1
-
106
-
-
84991528460
-
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
-
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, et al. (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience 2: 10.
-
(2013)
Gigascience
, vol.2
, pp. 10
-
-
Bradnam, K.R.1
Fass, J.N.2
Alexandrov, A.3
Baranay, P.4
Bechner, M.5
-
107
-
-
0003885423
-
-
(5th ed.). Addison Wesley Longman Publishing Co., Inc
-
Sommerville I (1995) Software engineering (5th ed.). Addison Wesley Longman Publishing Co., Inc. 742 p.
-
(1995)
Software engineering
, pp. 742
-
-
Sommerville, I.1
-
108
-
-
84869395032
-
NGS analyses by visualization with Trackster
-
Goecks J, Coraor N, Team TG, Nekrutenko A, Taylor J, (2012) NGS analyses by visualization with Trackster. Nat Biotech 30: 1036-1039.
-
(2012)
Nat Biotech
, vol.30
, pp. 1036-1039
-
-
Goecks, J.1
Coraor, N.2
Team, T.G.3
Nekrutenko, A.4
Taylor, J.5
-
109
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
-
110
-
-
84892692015
-
-
SAM (Sequence Alignment/Map) format. Available:. Accessed 16 August
-
SAM (Sequence Alignment/Map) format. Available: http://samtools.sourceforge.net/. Accessed 16 August 2013.
-
(2013)
-
-
-
111
-
-
84892707530
-
-
FASTG - An expressive representation for genome assemblies. Available:. Accessed 27 May
-
FASTG- An expressive representation for genome assemblies. Available: http://fastg.sourceforge.net/. Accessed 27 May 2013.
-
(2013)
-
-
|