-
1
-
-
1842717960
-
The Atlas genome assembly system
-
10.1101/gr.2264004, 383319, 15060016
-
Havlak P, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Weinstock GM, Gibbs RA. The Atlas genome assembly system. Genome Res 2004, 14(4):721-732. 10.1101/gr.2264004, 383319, 15060016.
-
(2004)
Genome Res
, vol.14
, Issue.4
, pp. 721-732
-
-
Havlak, P.1
Chen, R.2
Durbin, K.J.3
Egan, A.4
Ren, Y.5
Song, X.Z.6
Weinstock, G.M.7
Gibbs, R.A.8
-
2
-
-
0036144823
-
ARACHNE: a whole-genome shotgun assembler
-
10.1101/gr.208902, 155255, 11779843
-
Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. ARACHNE: a whole-genome shotgun assembler. Genome Res 2002, 12(1):177-189. 10.1101/gr.208902, 155255, 11779843.
-
(2002)
Genome Res
, vol.12
, Issue.1
, pp. 177-189
-
-
Batzoglou, S.1
Jaffe, D.B.2
Stanley, K.3
Butler, J.4
Gnerre, S.5
Mauceli, E.6
Berger, B.7
Mesirov, J.P.8
Lander, E.S.9
-
3
-
-
0034708758
-
A whole-genome assembly of Drosophila
-
10.1126/science.287.5461.2196, 10731133
-
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. A whole-genome assembly of Drosophila. Science 2000, 287(5461):2196-2204. 10.1126/science.287.5461.2196, 10731133.
-
(2000)
Science
, vol.287
, Issue.5461
, 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..
-
4
-
-
0141853948
-
PCAP: a whole-genome assembly program
-
10.1101/gr.1390403, 403719, 12952883
-
Huang X, Wang J, Aluru S, Yang SP, Hillier L. PCAP: a whole-genome assembly program. Genome Res 2003, 13(9):2164-2170. 10.1101/gr.1390403, 403719, 12952883.
-
(2003)
Genome Res
, vol.13
, Issue.9
, pp. 2164-2170
-
-
Huang, X.1
Wang, J.2
Aluru, S.3
Yang, S.P.4
Hillier, L.5
-
5
-
-
33847307402
-
Assembling millions of short DNA sequences using SSAKE
-
10.1093/bioinformatics/btl629, 17158514
-
Warren RL, Sutton GG, Jones SJ, Holt RA. Assembling millions of short DNA sequences using SSAKE. Bioinformatics 2007, 23(4):500-501. 10.1093/bioinformatics/btl629, 17158514.
-
(2007)
Bioinformatics
, vol.23
, Issue.4
, pp. 500-501
-
-
Warren, R.L.1
Sutton, G.G.2
Jones, S.J.3
Holt, R.A.4
-
6
-
-
35948929094
-
SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing
-
10.1101/gr.6435207, 2045152, 17908823
-
Dohm JC, Lottaz C, Borodina T, Himmelbauer H. SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res 2007, 17(11):1697-1706. 10.1101/gr.6435207, 2045152, 17908823.
-
(2007)
Genome Res
, vol.17
, Issue.11
, pp. 1697-1706
-
-
Dohm, J.C.1
Lottaz, C.2
Borodina, T.3
Himmelbauer, H.4
-
7
-
-
36448948250
-
Extending assembly of short DNA sequences to handle error
-
10.1093/bioinformatics/btm451, 17893086
-
Jeck WR, Reinhardt JA, Baltrus DA, Hickenbotham MT, Magrini V, Mardis ER, Dangl JL, Jones CD. Extending assembly of short DNA sequences to handle error. Bioinformatics 2007, 23(21):2942-2944. 10.1093/bioinformatics/btm451, 17893086.
-
(2007)
Bioinformatics
, vol.23
, Issue.21
, pp. 2942-2944
-
-
Jeck, W.R.1
Reinhardt, J.A.2
Baltrus, D.A.3
Hickenbotham, M.T.4
Magrini, V.5
Mardis, E.R.6
Dangl, J.L.7
Jones, C.D.8
-
8
-
-
69949167273
-
A fast hybrid short read fragment assembly algorithm
-
10.1093/bioinformatics/btp374, 19535537
-
Schmidt B, Sinha R, Beresford-Smith B, Puglisi SJ. A fast hybrid short read fragment assembly algorithm. Bioinformatics 2009, 25(17):2279-2280. 10.1093/bioinformatics/btp374, 19535537.
-
(2009)
Bioinformatics
, vol.25
, Issue.17
, pp. 2279-2280
-
-
Schmidt, B.1
Sinha, R.2
Beresford-Smith, B.3
Puglisi, S.J.4
-
9
-
-
0035859921
-
An Eulerian path approach to DNA fragment assembly
-
10.1073/pnas.171285098, 55524, 11504945
-
Pevzner PA, Tang H, Waterman MS. An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci USA 2001, 98(17):9748-9753. 10.1073/pnas.171285098, 55524, 11504945.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, Issue.17
, pp. 9748-9753
-
-
Pevzner, P.A.1
Tang, H.2
Waterman, M.S.3
-
10
-
-
39049156065
-
Short read fragment assembly of bacterial genomes
-
10.1101/gr.7088808, 2203630, 18083777
-
Chaisson MJ, Pevzner PA. Short read fragment assembly of bacterial genomes. Genome Res 2008, 18(2):324-330. 10.1101/gr.7088808, 2203630, 18083777.
-
(2008)
Genome Res
, vol.18
, Issue.2
, pp. 324-330
-
-
Chaisson, M.J.1
Pevzner, P.A.2
-
11
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
10.1101/gr.074492.107, 2336801, 18349386
-
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18(5):821-829. 10.1101/gr.074492.107, 2336801, 18349386.
-
(2008)
Genome Res
, vol.18
, Issue.5
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
12
-
-
43149086380
-
ALLPATHS: de novo assembly of whole-genome shotgun microreads
-
10.1101/gr.7337908, 2336810, 18340039
-
Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 2008, 18(5):810-820. 10.1101/gr.7337908, 2336810, 18340039.
-
(2008)
Genome Res
, vol.18
, Issue.5
, pp. 810-820
-
-
Butler, J.1
MacCallum, I.2
Kleber, M.3
Shlyakhter, I.A.4
Belmonte, M.K.5
Lander, E.S.6
Nusbaum, C.7
Jaffe, D.B.8
-
13
-
-
66449136667
-
ABySS: a parallel assembler for short read sequence data
-
10.1101/gr.089532.108, 2694472, 19251739
-
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. ABySS: a parallel assembler for short read sequence data. Genome Res 2009, 19(6):1117-1123. 10.1101/gr.089532.108, 2694472, 19251739.
-
(2009)
Genome Res
, vol.19
, Issue.6
, pp. 1117-1123
-
-
Simpson, J.T.1
Wong, K.2
Jackman, S.D.3
Schein, J.E.4
Jones, S.J.5
Birol, I.6
-
14
-
-
75649124547
-
De novo assembly of human genomes with massively parallel short read sequencing
-
10.1101/gr.097261.109, 2813482, 20019144
-
Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010, 20(2):265-272. 10.1101/gr.097261.109, 2813482, 20019144.
-
(2010)
Genome Res
, vol.20
, Issue.2
, pp. 265-272
-
-
Li, R.1
Zhu, H.2
Ruan, J.3
Qian, W.4
Fang, X.5
Shi, Z.6
Li, Y.7
Li, S.8
Shan, G.9
Kristiansen, K.10
Li, S.11
Yang, H.12
Wang, J.13
Wang, J.14
-
15
-
-
77952857079
-
Correction of sequencing errors in a maxed set of reads
-
10.1093/bioinformatics/btq151, 20378555
-
Salmela L. Correction of sequencing errors in a maxed set of reads. Bioinformatics 2010, 26(10):1284-1290. 10.1093/bioinformatics/btq151, 20378555.
-
(2010)
Bioinformatics
, vol.26
, Issue.10
, pp. 1284-1290
-
-
Salmela, L.1
-
16
-
-
69949178009
-
SHREC: a short read error correction method
-
Schröder J, Schröder H, Puglisi SJ, Sinha R, Schmidt B. SHREC: a short read error correction method. Bioinformatics 2009, 25(17):2157-2163.
-
(2009)
Bioinformatics
, vol.25
, Issue.17
, pp. 2157-2163
-
-
Schröder, J.1
Schröder, H.2
Puglisi, S.J.3
Sinha, R.4
Schmidt, B.5
-
17
-
-
74549205661
-
CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units
-
10.1186/1756-0500-2-73, 2694204, 19416548
-
Liu Y, Maskell DL, Schmidt B. CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units. BMC Research Notes 2009, 2:73. 10.1186/1756-0500-2-73, 2694204, 19416548.
-
(2009)
BMC Research Notes
, vol.2
, pp. 73
-
-
Liu, Y.1
Maskell, D.L.2
Schmidt, B.3
-
18
-
-
77951106340
-
CUDASW++ 2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions
-
10.1186/1756-0500-3-93, 2907862, 20370891
-
Liu Y, Schmidt B, Maskell DL. CUDASW++ 2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions. BMC Research Notes 2010, 3:93. 10.1186/1756-0500-3-93, 2907862, 20370891.
-
(2010)
BMC Research Notes
, vol.3
, pp. 93
-
-
Liu, Y.1
Schmidt, B.2
Maskell, D.L.3
-
20
-
-
77956339477
-
CUDA-MEME: accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units
-
Liu Y, Schmidt B, Liu W, Maskell DL. CUDA-MEME: accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units. Pattern Recognition Letters 2010, 31(14):2170-2177.
-
(2010)
Pattern Recognition Letters
, vol.31
, Issue.14
, pp. 2170-2177
-
-
Liu, Y.1
Schmidt, B.2
Liu, W.3
Maskell, D.L.4
-
21
-
-
77952001158
-
A parallel algorithm for error correction in high-throughput short-read data on CUDA-enabled graphics hardware
-
10.1089/cmb.2009.0062, 20426693
-
Shi H, Schmidt B, Liu W, Müller-Wittig W. A parallel algorithm for error correction in high-throughput short-read data on CUDA-enabled graphics hardware. J Comput Biol 2010, 17(4):603-615. 10.1089/cmb.2009.0062, 20426693.
-
(2010)
J Comput Biol
, vol.17
, Issue.4
, pp. 603-615
-
-
Shi, H.1
Schmidt, B.2
Liu, W.3
Müller-Wittig, W.4
-
22
-
-
0014814325
-
Space/time trade-offs in hash coding with allowable errors
-
Bloom BH. Space/time trade-offs in hash coding with allowable errors. Commu ACM 1970, 13:422-426.
-
(1970)
Commu ACM
, vol.13
, pp. 422-426
-
-
Bloom, B.H.1
-
23
-
-
78650262786
-
Quality-score guided error correction for short-read sequencing data using CUDA
-
Shi H, Schmidt B, Liu W, Müller-Wittig W. Quality-score guided error correction for short-read sequencing data using CUDA. Procedia Computer Science 2010, 1(1):1123-1132.
-
(2010)
Procedia Computer Science
, vol.1
, Issue.1
, pp. 1123-1132
-
-
Shi, H.1
Schmidt, B.2
Liu, W.3
Müller-Wittig, W.4
-
24
-
-
84888284964
-
Message Passing Interface (MPI) tutorial
-
Message Passing Interface (MPI) tutorial. , https://computing.llnl.gov/tutorials/mpi
-
-
-
-
25
-
-
84888284736
-
OpenMP tutorial
-
OpenMP tutorial. , https://computing.llnl.gov/tutorials/openMP
-
-
-
-
26
-
-
0034206002
-
Summary Cache: A Scalable Wide-Area Web Cache Sharing Protocol
-
Fan L, Cao P, Almeida J, Broder AZ. Summary Cache: A Scalable Wide-Area Web Cache Sharing Protocol. IEEE/ACM Transaction on Network 2000, 8:3.
-
(2000)
IEEE/ACM Transaction on Network
, vol.8
, pp. 3
-
-
Fan, L.1
Cao, P.2
Almeida, J.3
Broder, A.Z.4
-
27
-
-
78651550268
-
Scalable parallel programming with CUDA
-
Nickolls J, Buck I, Garland M, Skadron K. Scalable parallel programming with CUDA. ACM Queue 2008, 6(2):40-53.
-
(2008)
ACM Queue
, vol.6
, Issue.2
, pp. 40-53
-
-
Nickolls, J.1
Buck, I.2
Garland, M.3
Skadron, K.4
-
28
-
-
44849137198
-
NVIDIA Tesla: A unified graphics and computing architecture
-
Lindholm E, Nickolls J, Oberman S, Montrym J. NVIDIA Tesla: A unified graphics and computing architecture. IEEE Micro 2008, 28(2):39-55.
-
(2008)
IEEE Micro
, vol.28
, Issue.2
, pp. 39-55
-
-
Lindholm, E.1
Nickolls, J.2
Oberman, S.3
Montrym, J.4
-
29
-
-
77955858732
-
Fermi: NVIDIA's Next Generation CUDA Compute Architecture
-
NVIDIA
-
NVIDIA Fermi: NVIDIA's Next Generation CUDA Compute Architecture. NVIDIA., http://www.nvidia.com/content/PDF/fermi_white_papers/NVIDIA_Fermi_Compute_Architecture_Whitepaper.pdf
-
-
-
-
30
-
-
84874660404
-
NCBI homepage
-
NCBI homepage. , http://www.ncbi.nlm.nih.gov
-
-
-
-
31
-
-
84888285603
-
MVAPICH2 homepage
-
MVAPICH2 homepage. , http://mvapich.cse.ohio-state.edu/overview/mvapich2
-
-
-
-
32
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
10.1186/gb-2009-10-3-r25, 2690996, 19261174
-
Langmead B, Tranell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
-
(2009)
Genome Biology
, vol.10
-
-
Langmead, B.1
Tranell, C.2
Pop, M.3
Salzberg, S.L.4
|