-
1
-
-
41249096306
-
Using quality scores and longer reads improves accuracy of Solexa read mapping
-
Smith AD, Xuan Z, Zhang MQ (2008) Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics, 9: 128.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 128
-
-
Smith, A.D.1
Xuan, Z.2
Zhang, M.Q.3
-
2
-
-
55549097836
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores
-
Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18: 1851-1858.
-
(2008)
Genome Res.
, vol.18
, pp. 1851-1858
-
-
Li, H.1
Ruan, J.2
Durbin, R.3
-
3
-
-
70450177746
-
BFAST: An alignment tool for large scale genome resequencing
-
Homer N, Merriman B, Nelson SF (2009) BFAST: an alignment tool for large scale genome resequencing. Plos One, 4: e7767.
-
(2009)
Plos One
, vol.4
-
-
Homer, N.1
Merriman, B.2
Nelson, S.F.3
-
4
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10: R25.
-
(2009)
Genome Biol.
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
5
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25: 1755-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1755-1760
-
-
Li, H.1
Durbin, R.2
-
6
-
-
84864136658
-
CUSHAW: A CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform
-
Liu Y, Schmidt B, Maskell DL (2012) CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform. Bioinformatics, 28: 1830-1837.
-
(2012)
Bioinformatics
, vol.28
, pp. 1830-1837
-
-
Liu, Y.1
Schmidt, B.2
Maskell, D.L.3
-
7
-
-
84859048351
-
SOAP3: Ultra-fast GPU-based parallel alignment tool for short reads
-
Liu CM, Wong T, Wu E, Luo R, Yiu SM, et al. (2012) SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics, 28: 878-879.
-
(2012)
Bioinformatics
, vol.28
, pp. 878-879
-
-
Liu, C.M.1
Wong, T.2
Wu, E.3
Luo, R.4
Yiu, S.M.5
-
8
-
-
77949587649
-
Fast and accurate long-read alignment with Burrows-Wheeler transform
-
Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26: 589-595.
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
9
-
-
77957815609
-
GASSST: Global alignment short sequence search tool
-
Rizk G, Lavenier D (2010) GASSST: global alignment short sequence search tool. Bioinformatics, 26: 2534-2540.
-
(2010)
Bioinformatics
, vol.26
, pp. 2534-2540
-
-
Rizk, G.1
Lavenier, D.2
-
10
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg S (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods, 9: 357-359.
-
(2012)
Nature Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.2
-
11
-
-
84866447703
-
Long read alignment based on maximal exact match seeds
-
Liu Y, Schmidt B (2012) Long read alignment based on maximal exact match seeds. Bioinformatics, 28, i318-i324.
-
(2012)
Bioinformatics
, vol.28
-
-
Liu, Y.1
Schmidt, B.2
-
12
-
-
84870837088
-
The GEM mapper: Fast, accurate and versatile alignment by filtration
-
Marco-Sola S, Sammeth M, Guigó R, Ribeca P (2012) The GEM mapper: fast, accurate and versatile alignment by filtration. Nature Methods, 9: 1885-1888.
-
(2012)
Nature Methods
, vol.9
, pp. 1885-1888
-
-
Marco-Sola, S.1
Sammeth, M.2
Guigó, R.3
Ribeca, P.4
-
13
-
-
84866441562
-
Fast and accurate read alignment for resequencing
-
Mu JC, Jiang H, Kiani A, Mohiyuddin M, Bani Asadi N, et al. (2012) Fast and accurate read alignment for resequencing. Bioinformatics, 28: 2366-2373.
-
(2012)
Bioinformatics
, vol.28
, pp. 2366-2373
-
-
Mu, J.C.1
Jiang, H.2
Kiani, A.3
Mohiyuddin, M.4
Bani Asadi, N.5
-
14
-
-
84878532952
-
SOAP3-dp: Fast, accurate and sensitive GPU-based short-read aligner
-
Luo R, Wong T, Zhu J, Liu CM, Zhu X, et al. (2013) SOAP3-dp: fast, accurate and sensitive GPU-based short-read aligner. PLOS One, 8: e65632.
-
(2013)
PLOS One
, vol.8
-
-
Luo, R.1
Wong, T.2
Zhu, J.3
Liu, C.M.4
Zhu, X.5
-
16
-
-
77957272611
-
A survey of sequence alignment algorithms for next-generation sequencing
-
Li H, 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
-
17
-
-
79956307251
-
Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads
-
Lunter G, Goodson M (2011) Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res., 21: 936-939.
-
(2011)
Genome Res.
, vol.21
, pp. 936-939
-
-
Lunter, G.1
Goodson, M.2
-
18
-
-
0034764307
-
SSAHA: A fast search method for large DNA databases
-
DOI 10.1101/gr.194201
-
Ning Z, Cox AJ, Mullikin JC (2001) SSAHA: a fast search method for large DNA databases. Genome Res., 11: 1725-1729. (Pubitemid 33040499)
-
(2001)
Genome Research
, vol.11
, Issue.10
, pp. 1725-1729
-
-
Ning, Z.1
Cox, A.J.2
Mullikin, J.C.3
-
19
-
-
79953310937
-
SHRiMP2: Sensitive yet practical short read mapping
-
David M, Dzamba M, Lister D, Ilie L, Brudno M (2011) SHRiMP2: sensitive yet practical short read mapping. Bioinformatics, 27: 1011-1012.
-
(2011)
Bioinformatics
, vol.27
, pp. 1011-1012
-
-
David, M.1
Dzamba, M.2
Lister, D.3
Ilie, L.4
Brudno, M.5
-
20
-
-
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
-
21
-
-
84857145150
-
ART: A next-generation sequencing read simulator
-
Huang W, Li L, Myers JR, Marth GT (2012) ART: a next-generation sequencing read simulator. Bioinformatics, 28: 593-594.
-
(2012)
Bioinformatics
, vol.28
, pp. 593-594
-
-
Huang, W.1
Li, L.2
Myers, J.R.3
Marth, G.T.4
-
22
-
-
0031978181
-
Base-calling of automated sequencer traces using phred. II. Error probabilities
-
Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194. (Pubitemid 28177230)
-
(1998)
Genome Research
, vol.8
, Issue.3
, pp. 186-194
-
-
Ewing, B.1
Green, P.2
-
23
-
-
77956295988
-
The Genome Analysis Toolkit: A MapReduce framework for analyzing next generation DNA sequencing data
-
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next generation DNA sequencing data. Genome Res 20: 1297-1303.
-
(2010)
Genome Res
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
Hanna, M.2
Banks, E.3
Sivachenko, A.4
Cibulskis, K.5
-
26
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J. Mol. Biol., 147: 195-197.
-
(1981)
J. Mol. Biol.
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
|