-
1
-
-
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
-
2
-
-
33645781806
-
Cache-oblivious b-trees
-
Bender, M.A. et al. (2005) Cache-oblivious b-trees. SIAM J. Comput., 35, 341-358.
-
(2005)
SIAM J. Comput.
, vol.35
, pp. 341-358
-
-
Bender, M.A.1
-
3
-
-
0014814325
-
Space/time trade-offs in hash coding with allowable errors
-
Bloom, B.H. (1970) Space/time trade-offs in hash coding with allowable errors. Commun. ACM, 13, 422-426.
-
(1970)
Commun. ACM
, vol.13
, pp. 422-426
-
-
Bloom, B.H.1
-
4
-
-
84866687164
-
Space-efficient and exact de Bruijn graph representation based on a Bloom filter
-
Raphael, B. and Tang, T. (eds) Springer, Berlin, Heidelberg
-
Chikhi, R. and Rizk, G. (2012) Space-efficient and exact de Bruijn graph representation based on a Bloom filter. In: Raphael, B. and Tang, T. (eds) Algorithms in Bioinformatics, volume 7534 of Lecture Notes in Computer Science. Springer, Berlin, Heidelberg, pp. 236-248.
-
(2012)
Algorithms in Bioinformatics, Volume 7534 of Lecture Notes in Computer Science
, pp. 236-248
-
-
Chikhi, R.1
Rizk, G.2
-
5
-
-
80054732674
-
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets
-
Chitsaz, H. et al. (2011) Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat. Biotechnol., 29, 915-921.
-
(2011)
Nat. Biotechnol
, vol.29
, pp. 915-921
-
-
Chitsaz, H.1
-
6
-
-
84879028014
-
Disk-based k-mer counting on a PC
-
Deorowicz, S. et al. (2013) Disk-based k-mer counting on a PC. BMC Bioinformatics, 14, 160.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 160
-
-
Deorowicz, S.1
-
7
-
-
0034206002
-
Summary cache: A scalable wide-area web cache sharing protocol
-
Fan, L. et al. (2000) Summary cache: a scalable wide-area web cache sharing protocol. IEEE/ACM Trans. Netw., 8, 281-293.
-
(2000)
IEEE/ACM Trans. Netw.
, vol.8
, pp. 281-293
-
-
Fan, L.1
-
8
-
-
0037267048
-
Whole-genome sequence assembly for mammalian genomes: Arachne 2
-
Jaffe, D.B. et al. (2003) Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res., 13, 91-96.
-
(2003)
Genome Res.
, vol.13
, pp. 91-96
-
-
Jaffe, D.B.1
-
9
-
-
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
-
-
Kelley, D.R.1
-
11
-
-
84873307492
-
Musket: A multistage k-mer spectrum based error corrector for illumina sequence data
-
Liu, Y. et al. (2012) Musket: a multistage k-mer spectrum based error corrector for illumina sequence data. Bioinformatics, 29, 308-315.
-
(2012)
Bioinformatics
, vol.29
, pp. 308-315
-
-
Liu, Y.1
-
12
-
-
79952592810
-
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
-
Marcais, G. and Kingsford, C. (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics, 27, 764-770.
-
(2011)
Bioinformatics
, vol.27
, pp. 764-770
-
-
Marcais, G.1
Kingsford, C.2
-
13
-
-
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
-
-
Medvedev, P.1
-
14
-
-
81155158421
-
Efficient counting of k-mers in DNA sequences using a Bloom filter
-
Melsted, P. and Pritchard, J.K. (2011) Efficient counting of k-mers in DNA sequences using a Bloom filter. BMC Bioinformatics, 12, 333.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 333
-
-
Melsted, P.1
Pritchard, J.K.2
-
15
-
-
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
-
16
-
-
0003719406
-
-
2nd edn. Morgan Kaufmann Publishers, Inc., San Francisco, CA
-
Patterson, D.A. and Hennessey, J.L. (1998) Computer Organization and Design: the Hardware/Software Interface. 2nd edn. Morgan Kaufmann Publishers, Inc., San Francisco, CA.
-
(1998)
Computer Organization and Design: The Hardware/Software Interface
-
-
Patterson, D.A.1
Hennessey, J.L.2
-
17
-
-
84865176493
-
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs
-
[Epub ahead of print, doi:10.1073/pnas.1121464109, June 26, 2012]
-
Pell, J. et al. (2012) Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. Proc. Natl Acad. Sci. USA, [Epub ahead of print, doi:10.1073/pnas.1121464109, June 26, 2012].
-
(2012)
Proc. Natl Acad. Sci. USA
-
-
Pell, J.1
-
18
-
-
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
-
19
-
-
78149371810
-
Cache-, hash-, and space-efficient Bloom filters
-
Putze, F. et al. (2010) Cache-, hash-, and space-efficient Bloom filters. J. Exp. Algorithmics, 14, 4:4.4-4:4.18.
-
(2010)
J. Exp. Algorithmics
, vol.14
, pp. 4-18
-
-
Putze, F.1
-
20
-
-
84874741072
-
DSK: K-mer counting with very low memory usage
-
Rizk, G. et al. (2013) DSK: k-mer counting with very low memory usage. Bioinformatics, 29, 652-653.
-
(2013)
Bioinformatics
, vol.29
, pp. 652-653
-
-
Rizk, G.1
-
22
-
-
66449136667
-
Abyss: A parallel assembler for short read sequence data
-
Simpson, J.T. 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.T.1
-
23
-
-
84919446198
-
-
2nd edn. Addison-Wesley Professional
-
Warren, H.S. (2012) Hackers Delight. 2nd edn. Addison-Wesley Professional.
-
(2012)
Hackers Delight
-
-
Warren, H.S.1
-
24
-
-
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
|