-
1
-
-
84862591603
-
Toward almost closed genomes with gapfiller
-
Boetzer, M. and Pirovano, W. (2012) Toward almost closed genomes with gapfiller. Genome Biol., 13, R56.
-
(2012)
Genome Biol.
, vol.13
-
-
Boetzer, M.1
Pirovano, W.2
-
2
-
-
79951530130
-
Scaffolding pre-assembled contigs using sspace
-
Boetzer, M. et al. (2011) Scaffolding pre-assembled contigs using sspace. Bioinformatics, 27, 578-579.
-
(2011)
Bioinformatics
, vol.27
, pp. 578-579
-
-
Boetzer, M.1
-
3
-
-
39049156065
-
Short read fragment assembly of bacterial genomes
-
Chaisson, M.J. and Pevzner, P.A. (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
-
4
-
-
59949093527
-
De novo fragment assembly with short mate-paired reads: Does the read length matter?
-
Chaisson, M.J. et al. (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
-
5
-
-
77954324418
-
Sopra: Scaffolding algorithm for paired reads via statistical optimization
-
Dayarian, A. et al. (2010) Sopra: scaffolding algorithm for paired reads via statistical optimization. BMC Bioinformatics, 11, 345.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 345
-
-
Dayarian, A.1
-
6
-
-
35948929094
-
Sharcgs, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing
-
Dohm, J.C. et al. (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
-
7
-
-
80955159932
-
Opera: Reconstructing optimal genomic scaffolds with high-throughput paired-end sequences
-
Gao, S. et al. (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
-
8
-
-
70350012234
-
Assisted assembly: How to improve a de novo genome assembly by using related species
-
Gnerre, S. et al. (2009) Assisted assembly: how to improve a de novo genome assembly by using related species. Genome Biol., 10, R88.
-
(2009)
Genome Biol.
, vol.10
-
-
Gnerre, S.1
-
9
-
-
79952178131
-
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
-
Gnerre, S. et al. (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl Acad. Sci. USA, 108, 1513-1518.
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 1513-1518
-
-
Gnerre, S.1
-
10
-
-
84861749633
-
Grass: A generic algorithm for scaffolding next-generation sequencing assemblies
-
Gritsenko, A.A. et al. (2012) Grass: a generic algorithm for scaffolding next-generation sequencing assemblies. Bioinformatics, 28, 1429-1437.
-
(2012)
Bioinformatics
, vol.28
, pp. 1429-1437
-
-
Gritsenko, A.A.1
-
11
-
-
43149085041
-
De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer
-
Hernandez, D. et al. (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
-
12
-
-
79955468851
-
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
-
Hu, T.T. et al. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet., 43, 476-481.
-
(2011)
Nat. Genet.
, vol.43
, pp. 476-481
-
-
Hu, T.T.1
-
13
-
-
36448948250
-
Extending assembly of short DNA sequences to handle error
-
Jeck, W.R. 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
-
14
-
-
0036226603
-
Blatthe blast-like alignment tool
-
Kent, W. (2002) Blatthe blast-like alignment tool. Genome Res., 12, 656-664.
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.1
-
15
-
-
84873175933
-
Reference-assisted chromosome assembly
-
Kim, J. et al. (2013) Reference-assisted chromosome assembly. Proc. Natl Acad. Sci. USA, 110, 1785-1790.
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 1785-1790
-
-
Kim, J.1
-
16
-
-
84859210032
-
Fast gapped-read alignment with bowtie 2
-
Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with bowtie 2. Nat. Methods, 9, 357-359.
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
17
-
-
77957272611
-
A survey of sequence alignment algorithms for next-generation sequencing
-
Li, H. and Homer, N. (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief. Bioinform., 11, 473-483.
-
(2010)
Brief. Bioinform.
, vol.11
, pp. 473-483
-
-
Li, H.1
Homer, N.2
-
18
-
-
75649124547
-
De novo assembly of human genomes with massively parallel short read sequencing
-
Li, R. 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
-
19
-
-
79960411408
-
Comparative studies of de novo assembly tools for next-generation sequencing technologies
-
Lin, Y. 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
-
20
-
-
84942887758
-
Soapdenovo2: An empirically improved memory-efficient short-read de novo assembler
-
Luo, R. et al. (2012) Soapdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience, 1, 18.
-
(2012)
Gigascience
, vol.1
, pp. 18
-
-
Luo, R.1
-
21
-
-
80955139667
-
Paired de bruijn graphs: A novel approach for incorporating mate pair information into genome assemblers
-
Medvedev, P. et al. (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
-
22
-
-
57249105124
-
Aggressive assembly of pyrosequencing reads with mates
-
Miller, J.R. 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
-
23
-
-
57149099394
-
Sequencing of natural strains of Arabidopsis thaliana with short reads
-
Ossowski, S. et al. (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res., 18, 2024-2033.
-
(2008)
Genome Res.
, vol.18
, pp. 2024-2033
-
-
Ossowski, S.1
-
24
-
-
78650270346
-
Idba- A practical iterative de bruijn graph de novo assembler
-
Springer, Berlin Heidelberg
-
Peng, Y. et al. (2010) Idba- A practical iterative de bruijn graph de novo assembler. In: Research in Computational Molecular Biology. Springer, Berlin Heidelberg, pp. 426-440.
-
(2010)
Research in Computational Molecular Biology
, pp. 426-440
-
-
Peng, Y.1
-
25
-
-
0035859921
-
An eulerian path approach to dna fragment assembly
-
Pevzner, P. et al. (2001) An eulerian path approach to dna fragment assembly. Proc. Natl Acad. Sci. USA, 98, 9748.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 9748
-
-
Pevzner, P.1
-
26
-
-
45549109750
-
Genome assembly forensics: Finding the elusive mis-assembly
-
Phillippy, A.M. et al. (2008) Genome assembly forensics: finding the elusive mis-assembly. Genome Biol., 9, R55.
-
(2008)
Genome Biol.
, vol.9
-
-
Phillippy, A.M.1
-
27
-
-
16644381328
-
Comparative genome assembly
-
Pop, M. et al. (2004a) Comparative genome assembly. Brief. Bioinform., 5, 237-248.
-
(2004)
Brief. Bioinform.
, vol.5
, pp. 237-248
-
-
Pop, M.1
-
28
-
-
0346505466
-
Hierarchical scaffolding with bambus
-
Pop, M. et al. (2004b) Hierarchical scaffolding with bambus. Genome Res., 14, 149-159.
-
(2004)
Genome Res.
, vol.14
, pp. 149-159
-
-
Pop, M.1
-
29
-
-
84863519354
-
Sequel: Improving the accuracy of genome assemblies
-
Ronen, R. et al. (2012) Sequel: improving the accuracy of genome assemblies. Bioinformatics, 28, i188-i196.
-
(2012)
Bioinformatics
, vol.28
-
-
Ronen, R.1
-
30
-
-
82255185486
-
Fast scaffolding with small independent mixed integer programs
-
Salmela, L. et al. (2011) Fast scaffolding with small independent mixed integer programs. Bioinformatics, 27, 3259-3265.
-
(2011)
Bioinformatics
, vol.27
, pp. 3259-3265
-
-
Salmela, L.1
-
31
-
-
84857893016
-
Gage: A critical evaluation of genome assemblies and assembly algorithms
-
Salzberg, S.L. 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
-
32
-
-
84875591702
-
Hawkeye and AMOS: Visualizing and assessing the quality of genome assemblies
-
Schatz, M.C. et al. (2013) Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Brief. Bioinform., 14, 213-224.
-
(2013)
Brief. Bioinform.
, vol.14
, pp. 213-224
-
-
Schatz, M.C.1
-
33
-
-
79959974750
-
Reference-guided assembly of four diverse Arabidopsis thaliana genomes
-
Schneeberger, K. et al. (2011) Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc. Natl Acad. Sci. USA, 108, 10249-10254.
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 10249-10254
-
-
Schneeberger, K.1
-
34
-
-
66449136667
-
Abyss: A parallel assembler for short read sequence data
-
Simpson, J. 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.1
-
35
-
-
77950658346
-
Method improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
-
Tsai, I.J. et al. (2010) Method improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol., 11, R41.
-
(2010)
Genome Biol.
, vol.11
-
-
Tsai, I.J.1
-
36
-
-
33847307402
-
Assembling millions of short DNA sequences using ssake
-
Warren, R.L. et al. (2007) Assembling millions of short DNA sequences using ssake. Bioinformatics, 23, 500-501.
-
(2007)
Bioinformatics
, vol.23
, pp. 500-501
-
-
Warren, R.L.1
-
37
-
-
77955044283
-
SVDetect: A tool to identify genomic structural variations from paired-end and mate-pair sequencing data
-
Zeitouni, B. et al. (2010) SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinformatics, 26, 1895-1896.
-
(2010)
Bioinformatics
, vol.26
, pp. 1895-1896
-
-
Zeitouni, B.1
-
38
-
-
43149115851
-
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino, D. and 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.1
Birney, E.2
-
39
-
-
84885968059
-
The masurca genome assembler
-
Zimin, A.V. et al. (2013) The masurca genome assembler. Bioinformatics, 29, 2669-2677.
-
(2013)
Bioinformatics
, vol.29
, pp. 2669-2677
-
-
Zimin, A.V.1
|