-
1
-
-
85012046407
-
Robust error correction for de novo assembly via spectral partitioning and sequence alignment
-
Rojas,I. and Guzman,F.O. (eds), Copicentro Granada S.L., Granada, Spain
-
Alic,A. et al. (2014) Robust error correction for de novo assembly via spectral partitioning and sequence alignment. In:Rojas,I. and Guzman,F.O. (eds), Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO), Copicentro Granada S.L., Granada, Spain, pp. 1040-1048.
-
(2014)
Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO)
, pp. 1040-1048
-
-
Alic, A.1
-
2
-
-
84867121279
-
Improving PacBio long read accuracy by short read alignment
-
Au,K.F. et al. (2012) Improving PacBio long read accuracy by short read alignment. PLoS One, 7, e46679.
-
(2012)
PLoS One
, vol.7
-
-
Au, K.F.1
-
3
-
-
84860771820
-
SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
-
Bankevich,A. et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol., 19, 455-477.
-
(2012)
J. Comput. Biol.
, vol.19
, pp. 455-477
-
-
Bankevich, A.1
-
5
-
-
4544263565
-
Fragment assembly with short reads
-
Chaisson,M. et al. (2004) Fragment assembly with short reads. Bioinformatics, 20, 2067-2074.
-
(2004)
Bioinformatics
, vol.20
, pp. 2067-2074
-
-
Chaisson, M.1
-
6
-
-
84880798154
-
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
-
Chin,C.S. et al. (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods, 10, 563-569.
-
(2013)
Nat. Methods
, vol.10
, pp. 563-569
-
-
Chin, C.S.1
-
7
-
-
82255165034
-
Comparative analysis of algorithms for wholegenome assembly of pyrosequencing data
-
Finotello,F. et al. (2012) Comparative analysis of algorithms for wholegenome assembly of pyrosequencing data. Brief. Bioinformatics, 13, 269-280.
-
(2012)
Brief. Bioinformatics
, vol.13
, pp. 269-280
-
-
Finotello, F.1
-
8
-
-
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
-
9
-
-
84911416149
-
Blue: Correcting sequencing errors using consensus and context
-
Greenfield,P. et al. (2014) Blue: correcting sequencing errors using consensus and context. Bioinformatics, 30, 2723-2732.
-
(2014)
Bioinformatics
, vol.30
, pp. 2723-2732
-
-
Greenfield, P.1
-
10
-
-
84876266928
-
QUAST: Quality assessment tool for genome assemblies
-
Gurevich,A. et al. (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics, 29, 1072-1075.
-
(2013)
Bioinformatics
, vol.29
, pp. 1072-1075
-
-
Gurevich, A.1
-
11
-
-
84911372793
-
Proovread: Large-scale high-accuracy PacBio correction through iterative short read consensus
-
Hackl,T. et al. (2014) proovread: large-scale high-accuracy PacBio correction through iterative short read consensus. Bioinformatics, 30, 3004-3011.
-
(2014)
Bioinformatics
, vol.30
, pp. 3004-3011
-
-
Hackl, T.1
-
12
-
-
84900802154
-
BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads
-
Heo,Y. et al. (2014) BLESS: bloom filter-based error correction solution for high-throughput sequencing reads. Bioinformatics, 30, 1354-1362.
-
(2014)
Bioinformatics
, vol.30
, pp. 1354-1362
-
-
Heo, Y.1
-
13
-
-
84897110598
-
RACER: Rapid and accurate correction of errors in reads
-
Ilie,L. and Molnar,M. (2013) RACER: rapid and accurate correction of errors in reads. Bioinformatics, 29, 2490-2493.
-
(2013)
Bioinformatics
, vol.29
, pp. 2490-2493
-
-
Ilie, L.1
Molnar, M.2
-
14
-
-
79551589417
-
HiTEC: Accurate error correction in high-throughput sequencing data
-
Ilie,L. et al. (2011) HiTEC: accurate error correction in high-throughput sequencing data. Bioinformatics, 27, 295-302.
-
(2011)
Bioinformatics
, vol.27
, pp. 295-302
-
-
Ilie, L.1
-
15
-
-
79959867627
-
ECHO: A reference-free short-read error correction algorithm
-
Kao,W.C. et al. (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
-
16
-
-
78649358717
-
Quake: Quality-aware detection and correction of sequencing errors
-
Kelley,D.R. et al. (2010) Quake: quality-aware detection and correction of sequencing errors. Genome Biol., 11, R116.
-
(2010)
Genome Biol.
, vol.11
, pp. R116
-
-
Kelley, D.R.1
-
17
-
-
84900837285
-
Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures
-
Kleftogiannis,D. et al. (2013) Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures. PLoS One, 8, e75505.
-
(2013)
PLoS One
, vol.8
-
-
Kleftogiannis, D.1
-
18
-
-
84863651532
-
Hybrid error correction and de novo assembly of singlemolecule sequencing reads
-
Koren,S. et al. (2012) Hybrid error correction and de novo assembly of singlemolecule sequencing reads. Nat. Biotechnol., 30, 693-700.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 693-700
-
-
Koren, S.1
-
19
-
-
84878558449
-
Probabilistic error correction for RNA sequencing
-
Le,H.S. et al. (2013) Probabilistic error correction for RNA sequencing. Nucleic Acids Res., 41, e109.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. e109
-
-
Le, H.S.1
-
20
-
-
0036203448
-
Multiple sequence alignment using partial order graphs
-
Lee,C. et al. (2002) Multiple sequence alignment using partial order graphs. Bioinformatics, 18, 452-464.
-
(2002)
Bioinformatics
, vol.18
, pp. 452-464
-
-
Lee, C.1
-
21
-
-
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
-
22
-
-
84911413468
-
Trowel: A fast and accurate error correction module for Illumina sequencing reads
-
Lim,E.C. et al. (2014) Trowel: a fast and accurate error correction module for Illumina sequencing reads. Bioinformatics, 30, 3264-3265.
-
(2014)
Bioinformatics
, vol.30
, pp. 3264-3265
-
-
Lim, E.C.1
-
23
-
-
84873307492
-
Musket: A multistage k-mer spectrum-based error corrector for Illumina sequence data
-
Liu,Y. et al. (2013) Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. Bioinformatics, 29, 308-315.
-
(2013)
Bioinformatics
, vol.29
, pp. 308-315
-
-
Liu, Y.1
-
24
-
-
79959485321
-
Error correction of high-throughput sequencing datasets with non-uniform coverage
-
Medvedev,P. et al. (2011) Error correction of high-throughput sequencing datasets with non-uniform coverage. Bioinformatics, 27, i137-i141.
-
(2011)
Bioinformatics
, vol.27
, pp. i137-i141
-
-
Medvedev, P.1
-
25
-
-
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
-
26
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
-
(1970)
J. Mol. Biol.
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
27
-
-
84881309354
-
BayesHammer: Bayesian clustering for error correction in single-cell sequencing
-
Nikolenko,S.I. et al. (2013) BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics, 14(Suppl 1), S7.
-
(2013)
BMC Genomics
, vol.14
, pp. S7
-
-
Nikolenko, S.I.1
-
28
-
-
0018478882
-
Two algorithms for determining the most reliable path of a network
-
Petrovic,R. and Jovanovic,S. (1979) Two algorithms for determining the most reliable path of a network. IEEE Trans. Reliab., R-28, 115-119.
-
(1979)
IEEE Trans. Reliab.
, vol.R-28
, pp. 115-119
-
-
Petrovic, R.1
Jovanovic, S.2
-
29
-
-
0035859921
-
An Eulerian path approach to DNA fragment assembly
-
Pevzner,P.A. et al. (2001) An Eulerian path approach to DNA fragment assembly. Proc. Natl Acad. Sci. USA, 98, 9748-9753.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 9748-9753
-
-
Pevzner, P.A.1
-
30
-
-
67650074197
-
Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing
-
Qu,W. et al. (2009) Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing. Genome Res., 19, 1309-1315.
-
(2009)
Genome Res.
, vol.19
, pp. 1309-1315
-
-
Qu, W.1
-
31
-
-
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
-
32
-
-
84913539196
-
LoRDEC: Accurate and efficient long read error correction
-
Salmela,L. and Rivals,E. (2014) LoRDEC: accurate and efficient long read error correction. Bioinformatics, 30, 3506-3514.
-
(2014)
Bioinformatics
, vol.30
, pp. 3506-3514
-
-
Salmela, L.1
Rivals, E.2
-
33
-
-
79957814500
-
Correcting errors in short reads by multiple alignments
-
Salmela,L. and 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
-
34
-
-
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
-
35
-
-
69949178009
-
SHREC: A short-read error correction method
-
Schroder,J. et al. (2009) SHREC: a short-read error correction method. Bioinformatics, 25, 2157-2163.
-
(2009)
Bioinformatics
, vol.25
, pp. 2157-2163
-
-
Schroder, J.1
-
36
-
-
84907027898
-
Fiona: A parallel and automatic strategy for read error correction
-
Schulz,M.H. et al. (2014) Fiona: a parallel and automatic strategy for read error correction. Bioinformatics, 30, i356-i363.
-
(2014)
Bioinformatics
, vol.30
, pp. i356-i363
-
-
Schulz, M.H.1
-
37
-
-
84857838310
-
Efficient de novo assembly of large genomes using compressed data structures
-
Simpson,J.T. and 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
-
38
-
-
84965186660
-
Lighter: Fast and memory-efficient sequencing error correction without counting
-
Song,L. et al. (2014) Lighter: fast and memory-efficient sequencing error correction without counting. Genome Biol., 15, 509.
-
(2014)
Genome Biol.
, vol.15
, pp. 509
-
-
Song, L.1
-
39
-
-
77952973011
-
Recount: Expectation maximization based error correction tool for next generation sequencing data
-
Wijaya,E. et al. (2009) Recount: expectation maximization based error correction tool for next generation sequencing data. Genome Inform., 23, 189-201.
-
(2009)
Genome Inform.
, vol.23
, pp. 189-201
-
-
Wijaya, E.1
-
40
-
-
84900865525
-
HECTOR: A parallel multistage homopolymer spectrum based error corrector for 454 sequencing data
-
Wirawan,A. et al. (2014) HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. BMC Bioinformatics, 15, 131.
-
(2014)
BMC Bioinformatics
, vol.15
, pp. 131
-
-
Wirawan, A.1
-
41
-
-
77957758142
-
Reptile: Representative tiling for short read error correction
-
Yang,X. et al. (2010) Reptile: representative tiling for short read error correction. Bioinformatics, 26, 2526-2533.
-
(2010)
Bioinformatics
, vol.26
, pp. 2526-2533
-
-
Yang, X.1
-
42
-
-
79951539256
-
Repeat-aware modeling and correction of short read errors
-
Yang,X. et al. (2011) Repeat-aware modeling and correction of short read errors. BMC Bioinformatics, 12(Suppl 1), S52.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. S52
-
-
Yang, X.1
-
43
-
-
84865992574
-
A survey of error-correction methods for next-generation sequencing
-
Yang,X. et al. (2013) A survey of error-correction methods for next-generation sequencing. Brief. Bioinformatics, 14, 56-66.
-
(2013)
Brief. Bioinformatics
, vol.14
, pp. 56-66
-
-
Yang, X.1
-
44
-
-
43149115851
-
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino,D.R. 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.R.1
Birney, E.2
|