-
1
-
-
77954975104
-
Next-generation sequencing: adjusting to data overload
-
Baker M. Next-generation sequencing: adjusting to data overload. Nature Methods. 2010; 7. Available from: http://dx.doi.org/10.1038/nmeth0710-495
-
(2010)
Nature Methods
, vol.7
-
-
Baker, M.1
-
2
-
-
84876591284
-
Facing growth in the European Nucleotide Archive
-
Cochrane G, Alako B, Amid C, Bower L, Ana C, Cleland I, et al. Facing growth in the European Nucleotide Archive. Nucleic Acids Res. 2013;41(Database issue):D30-D35. Available from: http://dx.doi.org/10.1093/nar/gks1175
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.DATABASE ISSUE
, pp. D30-D35
-
-
Cochrane, G.1
Alako, B.2
Amid, C.3
Bower, L.4
Ana, C.5
Cleland, I.6
-
3
-
-
84856496549
-
Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis
-
Scholz M, Lo C, Chain P. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr Opin Biotechnol. 2012;23(1):9-15. Available from: http://dx.doi.org/10.1016/j.copbio.2011.11.013
-
(2012)
Curr Opin Biotechnol
, vol.23
, Issue.1
, pp. 9-15
-
-
Scholz, M.1
Lo, C.2
Chain, P.3
-
4
-
-
10344227692
-
Metagenomics: application of genomics to uncultured microorganisms
-
Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev: MMBR. 2004;68(4):669-85. Available from: http://dx.doi.org/10.1128/MMBR.68.4.669-685.2004
-
(2004)
Microbiol Mol Biol Rev: MMBR
, vol.68
, Issue.4
, pp. 669-685
-
-
Handelsman, J.1
-
5
-
-
79953007909
-
Microbial metagenomics: beyond the genome
-
Gilbert J, Dupont C. Microbial metagenomics: beyond the genome. Ann Rev Mar Sci. 2011;3:347-71. Available from: http://dx.doi.org/10.1146/annurev-marine-120709-142811
-
(2011)
Ann Rev Mar Sci
, vol.3
, pp. 347-371
-
-
Gilbert, J.1
Dupont, C.2
-
6
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin J, Li R, Raes J, Arumugam M, Burgdorf K, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59-65. Available from: http://dx.doi.org/10.1038/nature08821
-
(2010)
Nature
, vol.464
, Issue.7285
, pp. 59-65
-
-
Qin, J.1
Li, R.2
Raes, J.3
Arumugam, M.4
Burgdorf, K.5
Manichanh, C.6
-
7
-
-
35348968286
-
The human microbiome project
-
Turnbaugh P, Ley R, Hamady M, Claire F, Knight R, Gordon J. The human microbiome project. Nature. 2007;449(7164):804-810. Available from: http://dx.doi.org/10.1038/nature06244
-
(2007)
Nature
, vol.449
, Issue.7164
, pp. 804-810
-
-
Turnbaugh, P.1
Ley, R.2
Hamady, M.3
Claire, F.4
Knight, R.5
Gordon, J.6
-
8
-
-
83255181845
-
The Earth Microbiome Project: The meeting report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011
-
Gilbert JA, Bailey M, Field D, Fierer N, Fuhrman JA, Hu B, et al. The Earth Microbiome Project: The meeting report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011. Stand Genomic Sci. 2011;5(2):243
-
(2011)
Stand Genomic Sci
, vol.5
, Issue.2
, pp. 243
-
-
Gilbert, J.A.1
Bailey, M.2
Field, D.3
Fierer, N.4
Fuhrman, J.A.5
Hu, B.6
-
9
-
-
84906829581
-
The Earth Microbiome project: successes and aspirations
-
Gilbert J, Jansson J, Knight R. The Earth Microbiome project: successes and aspirations. BMC Biology. 2014;12(1):69
-
(2014)
BMC Biology
, vol.12
, Issue.1
, pp. 69
-
-
Gilbert, J.1
Jansson, J.2
Knight, R.3
-
10
-
-
84946041374
-
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification
-
Reddy TBK, Thomas AD, Stamatis D, Bertsch J, Isbandi M, Jansson J, et al. The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. Nucleic Acids Res. 2014. Available from: http://dx.doi.org/10.1093/nar/gku950
-
(2014)
Nucleic Acids Res
-
-
Reddy, T.B.K.1
Thomas, A.D.2
Stamatis, D.3
Bertsch, J.4
Isbandi, M.5
Jansson, J.6
-
11
-
-
0036677450
-
Estimating prokaryotic diversity and its limits
-
Curtis T, Sloan W, Scannell J. Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USAs. 2002;99(16):10494-9. Available from: http://dx.doi.org/10.1073/pnas.142680199
-
(2002)
Proc Natl Acad Sci USAs
, vol.99
, Issue.16
, pp. 10494-10499
-
-
Curtis, T.1
Sloan, W.2
Scannell, J.3
-
12
-
-
77957272611
-
A survey of sequence alignment algorithms for next-generation sequencing
-
Li H, Homer N. A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform. 2010;11(5):473-83. Available from: http://dx.doi.org/10.1093/bib/bbq015
-
(2010)
Brief Bioinform
, vol.11
, Issue.5
, pp. 473-483
-
-
Li, H.1
Homer, N.2
-
13
-
-
84878629521
-
Benchmarking short sequence mapping tools
-
Hatem A, Bozdag D, Toland A, çatalyürek UV. Benchmarking short sequence mapping tools. BMC Bioinforma. 2013;14(1):184. Available from: http://dx.doi.org/10.1186/1471-2105-14-184
-
(2013)
BMC Bioinforma
, vol.14
, Issue.1
, pp. 184
-
-
Hatem, A.1
Bozdag, D.2
Toland, A.3
Çatalyürek, U.V.4
-
14
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul S, Madden T, Schäffer A, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389-402. Available from: http://dx.doi.org/10.1093/nar/25.17.3389
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.1
Madden, T.2
Schäffer, A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
-
15
-
-
0036083631
-
BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster
-
Grant J, Dunbrack R, Manion F, Ochs M. BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster. Bioinformatics (Oxford, England). 2002;18(5):765-6. Available from: http://dx.doi.org/10.1093/bioinformatics/18.5.765
-
(2002)
Bioinformatics (Oxford, England)
, vol.18
, Issue.5
, pp. 765-766
-
-
Grant, J.1
Dunbrack, R.2
Manion, F.3
Ochs, M.4
-
16
-
-
25444481798
-
Squid-a simple bioinformatics grid
-
Carvalho P, Glória R, de Miranda A, Degrave W. Squid-a simple bioinformatics grid. BMC bioinforma. 2005;6(1):197. Available from: http://dx.doi.org/10.1186/1471-2105-6-197
-
(2005)
BMC bioinforma
, vol.6
, Issue.1
, pp. 197
-
-
Carvalho, P.1
Glória, R.2
de Miranda, A.3
Degrave, W.4
-
17
-
-
59349099504
-
G-BLAST: a Grid-based solution for mpiBLAST on computational Grids
-
Yang C, Han T, Kan H. G-BLAST: a Grid-based solution for mpiBLAST on computational Grids. Concurr Comput: Pract Exper. 2009;21(2):225-55. Available from: http://dx.doi.org/10.1002/cpe.1346
-
(2009)
Concurr Comput: Pract Exper
, vol.21
, Issue.2
, pp. 225-255
-
-
Yang, C.1
Han, T.2
Kan, H.3
-
18
-
-
33746047855
-
The design, implementation, and evaluation of mpiBLAST (Best Paper: Applications Track)
-
Darling A, Carey L, Feng WC. The design, implementation, and evaluation of mpiBLAST (Best Paper: Applications Track). 4th International Conference on Linux Clusters: The HPC Revolution 2003 in conjunction with ClusterWorld Conference & Expo. 2003:14
-
(2003)
4th International Conference on Linux Clusters: The HPC Revolution 2003 in conjunction with ClusterWorld Conference & Expo
, pp. 14
-
-
Darling, A.1
Carey, L.2
Feng, W.C.3
-
19
-
-
0141840819
-
Soap-HT-BLAST: high throughput BLAST based on Web services
-
Wang J, Mu Q. Soap-HT-BLAST: high throughput BLAST based on Web services. Bioinformatics (Oxford, England). 2003;19(14):1863-4. Available from: http://dx.doi.org/10.1093/bioinformatics/btg244
-
(2003)
Bioinformatics (Oxford, England)
, vol.19
, Issue.14
, pp. 1863-1864
-
-
Wang, J.1
Mu, Q.2
-
20
-
-
25444459890
-
Windows .NET network distributed basic local alignment search toolkit (W.ND-BLAST)
-
Dowd S, Zaragoza J, Rodriguez J, Oliver M, Payton P. Windows .NET network distributed basic local alignment search toolkit (W.ND-BLAST). BMC bioinformatics. 2005;6(1):93. Available from: http://dx.doi.org/10.1186/1471-2105-6-93
-
(2005)
BMC bioinformatics
, vol.6
, Issue.1
, pp. 93
-
-
Dowd, S.1
Zaragoza, J.2
Rodriguez, J.3
Oliver, M.4
Payton, P.5
-
21
-
-
80052121849
-
CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing
-
Angiuoli SV, Matalka M, Gussman A, Galens K, Vangala M, Riley DR, et al. CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC bioinformatics. 2011;12(1):356
-
(2011)
BMC bioinformatics
, vol.12
, Issue.1
, pp. 356
-
-
Angiuoli, S.V.1
Matalka, M.2
Gussman, A.3
Galens, K.4
Vangala, M.5
Riley, D.R.6
-
22
-
-
84883001733
-
DistMap: A toolkit for distributed short read mapping on a hadoop cluster
-
08
-
Pandey RV, Schlötterer C. DistMap: A toolkit for distributed short read mapping on a hadoop cluster. PLoS ONE. 2013 08;8(8):e72614. Available from: http://dx.doi.org/10.1371/journal.pone.0072614
-
(2013)
PLoS ONE
, vol.8
, Issue.8
-
-
Pandey, R.V.1
Schlötterer, C.2
-
23
-
-
65649120715
-
CloudBurst: highly sensitive read mapping with MapReduce
-
Schatz M. CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics (Oxford, England). 2009;25(11):1363-9. Available from: http://dx.doi.org/10.1093/bioinformatics/btp236
-
(2009)
Bioinformatics (Oxford, England)
, vol.25
, Issue.11
, pp. 1363-1369
-
-
Schatz, M.1
-
24
-
-
79957895842
-
CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping
-
Nguyen T, Shi W, Ruden D. CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping. BMC research notes. 2011;4(1):171. Available from: http://dx.doi.org/10.1186/1756-0500-4-171
-
(2011)
BMC research notes
, vol.4
, Issue.1
, pp. 171
-
-
Nguyen, T.1
Shi, W.2
Ruden, D.3
-
25
-
-
84898639657
-
STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud
-
01
-
Karczewski KJ, Fernald GH, Martin AR, Snyder M, Tatonetti NP, Dudley JT. STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud. PLoS ONE. 2014 01;9(1):e84860. Available from:http://dx.doi.org/10.1371/journal.pone.0084860
-
(2014)
PLoS ONE
, vol.9
, Issue.1
-
-
Karczewski, K.J.1
Fernald, G.H.2
Martin, A.R.3
Snyder, M.4
Tatonetti, N.P.5
Dudley, J.T.6
-
26
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335-6
-
(2010)
Nat Methods
, vol.7
, Issue.5
, pp. 335-336
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
Bittinger, K.4
Bushman, F.D.5
Costello, E.K.6
-
27
-
-
84991528983
-
-
Accessed 22 Aug 2015
-
iMatix Corporation. ZeroMQ. 2014. Available from: http://www.zeromq. org/.Accessed 22 Aug 2015
-
(2014)
ZeroMQ
-
-
-
28
-
-
84874604550
-
-
Accessed 22 Aug 2015
-
Hannon lab. FASTX-Toolkit. 2014. Available from: http://hannonlab.cshl.edu/fastx_toolkit. Accessed 22 Aug 2015
-
(2014)
FASTX-Toolkit
-
-
-
29
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nat methods. 2012;9(4):357-359. Available from: http://dx.doi.org/10.1038/nmeth.1923
-
(2012)
Nat methods
, vol.9
, Issue.4
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.2
-
30
-
-
0036226603
-
BLAT-the BLAST-like alignment tool
-
Kent W. BLAT-the BLAST-like alignment tool. Genome res. 2002;12(4): 656-664. Available from: http://dx.doi.org/10.1101/gr.229202
-
(2002)
Genome res
, vol.12
, Issue.4
, pp. 656-664
-
-
Kent, W.1
-
32
-
-
84870837088
-
The GEM mapper: fast, accurate and versatile alignment by filtration
-
Santiago M, Sammeth M, Guigó R, Ribeca P. The GEM mapper: fast, accurate and versatile alignment by filtration. Nat methods. 2012;9(12): 1185-8. Available from: http://dx.doi.org/10.1038/nmeth.2221
-
(2012)
Nat methods
, vol.9
, Issue.12
, pp. 1185-1188
-
-
Santiago, M.1
Sammeth, M.2
Guigó, R.3
Ribeca, P.4
-
33
-
-
84870471176
-
RazerS 3 faster, fully sensitive read mapping
-
Weese D, Holtgrewe M, Reinert K. RazerS 3 faster, fully sensitive read mapping. Bioinformatics (Oxford, England). 2012;28(20):2592-9. Available from: http://dx.doi.org/10.1093/bioinformatics/bts505
-
(2012)
Bioinformatics (Oxford, England)
, vol.28
, Issue.20
, pp. 2592-2599
-
-
Weese, D.1
Holtgrewe, M.2
Reinert, K.3
-
34
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26(19):2460-1
-
(2010)
Bioinformatics
, vol.26
, Issue.19
, pp. 2460-2461
-
-
Edgar, R.C.1
-
35
-
-
84991527845
-
-
Accessed 22 Aug 2015
-
Boulund F, Sjögren A, Kristiansson E. Tentacle. 2014. Available from: http://bioinformatics.math.chalmers.se/tentacle/. Accessed 22 Aug 2015
-
(2014)
-
-
Boulund, F.1
Sjögren, A.2
Tentacle, K.E.3
-
36
-
-
84991528710
-
-
Accessed 22 Aug 2015
-
Sched MD. Slurm. 2014. Available from: http://slurm.schedmd.com/. Accessed 22 Aug 2015
-
(2014)
Slurm
-
-
Sched, M.D.1
-
37
-
-
34247481878
-
IPython: a System for Interactive Scientific Computing
-
May. Accessed 22 Aug 2015
-
Pérez F, Granger BE. IPython: a System for Interactive Scientific Computing. Comput Sci Eng. 2007 May;9(3):21-9. Available from: http://ipython.org. Accessed 22 Aug 2015
-
(2007)
Comput Sci Eng
, vol.9
, Issue.3
, pp. 21-29
-
-
Pérez, F.1
Granger, B.E.2
-
40
-
-
84971378599
-
-
Version 3.0
-
Forum MPI. MPI: A message-passing interface standard. Version 3.0. 2012. Available from: http://www.mpi-forum.org/docs/mpi-3.0/mpi30-report.pdf
-
(2012)
MPI: A message-passing interface standard
-
-
-
41
-
-
77949275829
-
Reliability of a System of k Nodes for High Performance Computing Applications
-
Gottumukkala N, Nassar R, Paun M, Leangsuksun C, Scott S. Reliability of a System of k Nodes for High Performance Computing Applications. IEEE Trans Reliab. 2010;59(1):162-9. Available from: http://dx.doi.org/10.1109/TR.2009.2034291
-
(2010)
IEEE Trans Reliab
, vol.59
, Issue.1
, pp. 162-169
-
-
Gottumukkala, N.1
Nassar, R.2
Paun, M.3
Leangsuksun, C.4
Scott, S.5
-
42
-
-
77950347409
-
A view of cloud computing
-
Armbrust M, Fox A, Griffith R, Joseph AD, Katz R, Konwinski A, et al. A view of cloud computing. Commun ACM. 2010;53(4):50-8
-
(2010)
Commun ACM
, vol.53
, Issue.4
, pp. 50-58
-
-
Armbrust, M.1
Fox, A.2
Griffith, R.3
Joseph, A.D.4
Katz, R.5
Konwinski, A.6
-
43
-
-
37549003336
-
MapReduce: simplified data processing on large clusters
-
Dean J, Ghemawat S. MapReduce: simplified data processing on large clusters. Commun ACM. 2008;51(1):107-13
-
(2008)
Commun ACM
, vol.51
, Issue.1
, pp. 107-113
-
-
Dean, J.1
Ghemawat, S.2
-
44
-
-
74049113467
-
-
Sebastobol, California: O'Reilly Media, Inc
-
White T. Hadoop: The definitive guide. Sebastobol, California: O'Reilly Media, Inc; 2012
-
(2012)
Hadoop: The definitive guide
-
-
White, T.1
-
45
-
-
84870020971
-
Classification of metagenomic sequences: methods and challenges
-
Mande S, Mohammed M, Ghosh T. Classification of metagenomic sequences: methods and challenges. Brief Bioinform. 2012;13(6):669-81. Available from: http://dx.doi.org/10.1093/bib/bbs054
-
(2012)
Brief Bioinform
, vol.13
, Issue.6
, pp. 669-681
-
-
Mande, S.1
Mohammed, M.2
Ghosh, T.3
-
46
-
-
84862524261
-
Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis
-
Schbath S, Martin V, Zytnicki M, Fayolle J, Loux V, Gibrat J. Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. J Comput Biol: J Mol Cell Biol. 2012;19(6):796-813. Available from: http://dx.doi.org/10.1089/cmb.2012.0022
-
(2012)
J Comput Biol: J Mol Cell Biol
, vol.19
, Issue.6
, pp. 796-813
-
-
Schbath, S.1
Martin, V.2
Zytnicki, M.3
Fayolle, J.4
Loux, V.5
Gibrat, J.6
-
47
-
-
84905003668
-
DSRC 2-Industry-oriented compression of FASTQ files
-
Roguski L, Deorowicz S. DSRC 2-Industry-oriented compression of FASTQ files. Bioinformatics. 2014;30(15):2213-5. Available from: http://dx.doi.org/10.1093/bioinformatics/btu208
-
(2014)
Bioinformatics
, vol.30
, Issue.15
, pp. 2213-2215
-
-
Roguski, L.1
Deorowicz, S.2
-
48
-
-
0022238527
-
Improvements in Multiprocessor System Design
-
Jun
-
Rodgers DP. Improvements in Multiprocessor System Design. SIGARCH Comput Archit News. 1985 Jun;13(3):225-31. Available from: http://doi.acm.org/10.1145/327070.327215
-
(1985)
SIGARCH Comput Archit News
, vol.13
, Issue.3
, pp. 225-231
-
-
Rodgers, D.P.1
-
49
-
-
53549118607
-
The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes
-
Meyer F, Paarmann D, D'Souza M, Olson R, Glass E, Kubal M, et al. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9:386
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 386
-
-
Meyer, F.1
Paarmann, D.2
D'Souza, M.3
Olson, R.4
Glass, E.5
Kubal, M.6
-
50
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Available from: http://genomebiology.com/2009/10/3/R25
-
(2009)
Genome Biol
, vol.10
, Issue.3
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.4
-
53
-
-
84991527005
-
-
1928 Diagnostics. Resqu. Accessed 22 Aug 2015
-
Kristiansson E. 1928 Diagnostics. Resqu. 2014. Available from: http://www.1928diagnostics.com/resdb/. Accessed 22 Aug 2015
-
(2014)
-
-
Kristiansson, E.1
|