-
1
-
-
77952886150
-
Assembly algorithms for next-generation sequencing data
-
10.1016/j.ygeno.2010.03.001, 2874646, 20211242
-
Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics 2010, 95(6):315-327. 10.1016/j.ygeno.2010.03.001, 2874646, 20211242.
-
(2010)
Genomics
, vol.95
, Issue.6
, pp. 315-327
-
-
Miller, J.R.1
Koren, S.2
Sutton, G.3
-
2
-
-
70349212271
-
Parametric complexity of sequence assembly: theory and applications to next generation sequencing
-
10.1089/cmb.2009.0005, 19580519
-
Nagarajan N, Pop M. Parametric complexity of sequence assembly: theory and applications to next generation sequencing. J Comput Biol 2009, 16(7):897-908. 10.1089/cmb.2009.0005, 19580519.
-
(2009)
J Comput Biol
, vol.16
, Issue.7
, pp. 897-908
-
-
Nagarajan, N.1
Pop, M.2
-
3
-
-
84874194145
-
Sequence assembly demystified
-
10.1038/nrg3367, 23358380
-
Nagarajan N, Pop M. Sequence assembly demystified. Nat Rev Genet 2013, 14(3):157-167. 10.1038/nrg3367, 23358380.
-
(2013)
Nat Rev Genet
, vol.14
, Issue.3
, pp. 157-167
-
-
Nagarajan, N.1
Pop, M.2
-
4
-
-
0029312158
-
Toward simplifying and accurately formulating fragment assembly
-
10.1089/cmb.1995.2.275, 7497129
-
Myers EW. Toward simplifying and accurately formulating fragment assembly. J Comput Biol 1995, 2(2):275-290. 10.1089/cmb.1995.2.275, 7497129.
-
(1995)
J Comput Biol
, vol.2
, Issue.2
, pp. 275-290
-
-
Myers, E.W.1
-
5
-
-
84991528460
-
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
-
10.1186/2047-217X-2-10, 3844414, 23870653
-
Bradnam K, Fass J, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman J, Chapuis G, Chikhi R, Chitsaz H, Chou W-C, Corbeil J, Del Fabbro C, Docking T, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca N, Ganapathy G, Gibbs R, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt J, Ho I. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience 2013, 2(1):10. 10.1186/2047-217X-2-10, 3844414, 23870653.
-
(2013)
GigaScience
, vol.2
, Issue.1
, pp. 10
-
-
Bradnam, K.1
Fass, J.2
Alexandrov, A.3
Baranay, P.4
Bechner, M.5
Birol, I.6
Boisvert, S.7
Chapman, J.8
Chapuis, G.9
Chikhi, R.10
Chitsaz, H.11
Chou, W.-C.12
Corbeil, J.13
Del Fabbro, C.14
Docking, T.15
Durbin, R.16
Earl, D.17
Emrich, S.18
Fedotov, P.19
Fonseca, N.20
Ganapathy, G.21
Gibbs, R.22
Gnerre, S.23
Godzaridis, E.24
Goldstein, S.25
Haimel, M.26
Hall, G.27
Haussler, D.28
Hiatt, J.29
Ho, I.30
more..
-
6
-
-
83055181941
-
Assemblathon 1: a competitive assessment of de novo short read assembly methods
-
10.1101/gr.126599.111, 3227110, 21926179
-
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol I, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res 2011, 21(12):2224-2241. 10.1101/gr.126599.111, 3227110, 21926179.
-
(2011)
Genome Res
, vol.21
, Issue.12
, pp. 2224-2241
-
-
Earl, D.1
Bradnam, K.2
St John, J.3
Darling, A.4
Lin, D.5
Fass, J.6
Yu, H.O.7
Buffalo, V.8
Zerbino, D.R.9
Diekhans, M.10
Nguyen, N.11
Ariyaratne, P.N.12
Sung, W.K.13
Ning, Z.14
Haimel, M.15
Simpson, J.T.16
Fonseca, N.A.17
Birol, I.18
Docking, T.R.19
Ho, I.Y.20
Rokhsar, D.S.21
Chikhi, R.22
Lavenier, D.23
Chapuis, G.24
Naquin, D.25
Maillet, N.26
Schatz, M.C.27
Kelley, D.R.28
Phillippy, A.M.29
Koren, S.30
more..
-
7
-
-
84857893016
-
GAGE: a critical evaluation of genome assemblies and assembly algorithms
-
10.1101/gr.131383.111, 3290791, 22147368
-
Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M. GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res 2012, 22(3):557-567. 10.1101/gr.131383.111, 3290791, 22147368.
-
(2012)
Genome Res
, vol.22
, Issue.3
, pp. 557-567
-
-
Salzberg, S.L.1
Phillippy, A.M.2
Zimin, A.3
Puiu, D.4
Magoc, T.5
Koren, S.6
Treangen, T.J.7
Schatz, M.C.8
Delcher, A.L.9
Roberts, M.10
-
8
-
-
84880196418
-
GAGE-B: an evaluation of genome assemblers for bacterial organisms
-
10.1093/bioinformatics/btt273, 3702249, 23665771
-
Magoc T, Pabinger S, Canzar S, Liu X, Su Q, Puiu D, Tallon LJ, Salzberg SL. GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics 2013, 29(14):1718-1725. 10.1093/bioinformatics/btt273, 3702249, 23665771.
-
(2013)
Bioinformatics
, vol.29
, Issue.14
, pp. 1718-1725
-
-
Magoc, T.1
Pabinger, S.2
Canzar, S.3
Liu, X.4
Su, Q.5
Puiu, D.6
Tallon, L.J.7
Salzberg, S.L.8
-
9
-
-
45549109750
-
Genome assembly forensics: finding the elusive mis-assembly
-
10.1186/gb-2008-9-3-r55, 2397507, 18341692
-
Phillippy AM, Schatz MC, Pop M. Genome assembly forensics: finding the elusive mis-assembly. Genome Biol 2008, 9(3):R55-R55. 10.1186/gb-2008-9-3-r55, 2397507, 18341692.
-
(2008)
Genome Biol
, vol.9
, Issue.3
-
-
Phillippy, A.M.1
Schatz, M.C.2
Pop, M.3
-
10
-
-
84874322149
-
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
-
10.1093/bioinformatics/bts723, 23303509
-
Clark SC, Egan R, Frazier PI, Wang Z. ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies. Bioinformatics 2013, 29(4):435-443. 10.1093/bioinformatics/bts723, 23303509.
-
(2013)
Bioinformatics
, vol.29
, Issue.4
, pp. 435-443
-
-
Clark, S.C.1
Egan, R.2
Frazier, P.I.3
Wang, Z.4
-
11
-
-
84872968454
-
CGAL: computing genome assembly likelihoods
-
10.1186/gb-2013-14-1-r8, 3663106, 23360652
-
Rahman A, Pachter L. CGAL: computing genome assembly likelihoods. Genome Biol 2013, 14(1):R8. 10.1186/gb-2013-14-1-r8, 3663106, 23360652.
-
(2013)
Genome Biol
, vol.14
, Issue.1
-
-
Rahman, A.1
Pachter, L.2
-
12
-
-
84878076144
-
REAPR: a universal tool for genome assembly evaluation
-
10.1186/gb-2013-14-5-r47, 3798757, 23710727
-
Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD. REAPR: a universal tool for genome assembly evaluation. Genome Biol 2013, 14(5):R47. 10.1186/gb-2013-14-5-r47, 3798757, 23710727.
-
(2013)
Genome Biol
, vol.14
, Issue.5
-
-
Hunt, M.1
Kikuchi, T.2
Sanders, M.3
Newbold, C.4
Berriman, M.5
Otto, T.D.6
-
13
-
-
84876266928
-
QUAST: quality assessment tool for genome assemblies
-
10.1093/bioinformatics/btt086, 3624806, 23422339
-
Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013, 29(8):1072-1075. 10.1093/bioinformatics/btt086, 3624806, 23422339.
-
(2013)
Bioinformatics
, vol.29
, Issue.8
, pp. 1072-1075
-
-
Gurevich, A.1
Saveliev, V.2
Vyahhi, N.3
Tesler, G.4
-
14
-
-
84882295406
-
De novo likelihood-based measures for assembly validation
-
10.1186/1756-0500-6-334, 3765854, 23965294
-
Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M. De novo likelihood-based measures for assembly validation. BMC Res Notes 2013, 6(1):334. 10.1186/1756-0500-6-334, 3765854, 23965294.
-
(2013)
BMC Res Notes
, vol.6
, Issue.1
, pp. 334
-
-
Ghodsi, M.1
Hill, C.M.2
Astrovskaya, I.3
Lin, H.4
Sommer, D.D.5
Koren, S.6
Pop, M.7
-
15
-
-
84871686918
-
Reevaluating assembly evaluations with feature response curves: GAGE and assemblathons
-
10.1371/journal.pone.0052210, 3532452, 23284938
-
Vezzi F, Narzisi G, Mishra B. Reevaluating assembly evaluations with feature response curves: GAGE and assemblathons. PLoS One 2012, 7(12):e52210. 10.1371/journal.pone.0052210, 3532452, 23284938.
-
(2012)
PLoS One
, vol.7
, Issue.12
-
-
Vezzi, F.1
Narzisi, G.2
Mishra, B.3
-
16
-
-
84890056084
-
Toward a statistically explicit understanding of de novo sequence assembly
-
10.1093/bioinformatics/btt525, 24021385
-
Howison M, Zapata F, Dunn CW. Toward a statistically explicit understanding of de novo sequence assembly. Bioinformatics 2013, 29(23):2959-2963. 10.1093/bioinformatics/btt525, 24021385.
-
(2013)
Bioinformatics
, vol.29
, Issue.23
, pp. 2959-2963
-
-
Howison, M.1
Zapata, F.2
Dunn, C.W.3
-
17
-
-
84866391549
-
An integrated pipeline for de novo assembly of microbial genomes
-
10.1371/journal.pone.0042304, 3441570, 23028432
-
Tritt A, Eisen JA, Facciotti MT, Darling AE. An integrated pipeline for de novo assembly of microbial genomes. PLoS One 2012, 7(9):e42304. 10.1371/journal.pone.0042304, 3441570, 23028432.
-
(2012)
PLoS One
, vol.7
, Issue.9
-
-
Tritt, A.1
Eisen, J.A.2
Facciotti, M.T.3
Darling, A.E.4
-
18
-
-
84901407841
-
A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data
-
arXiv preprint arXiv:1401.5130 2014
-
Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. arXiv preprint arXiv:1401.5130 2014.
-
-
-
Coil, D.1
Jospin, G.2
Darling, A.E.3
-
19
-
-
77955032305
-
A computational genomics pipeline for prokaryotic sequencing projects
-
10.1093/bioinformatics/btq284, 2905547, 20519285
-
Kislyuk AO, Katz LS, Agrawal S, Hagen MS, Conley AB, Jayaraman P, Nelakuditi V, Humphrey JC, Sammons SA, Govil D, Mair RD, Tatti KM, Tondella ML, Harcourt BH, Mayer LW, Jordan IK. A computational genomics pipeline for prokaryotic sequencing projects. Bioinformatics 2010, 26(15):1819-1826. 10.1093/bioinformatics/btq284, 2905547, 20519285.
-
(2010)
Bioinformatics
, vol.26
, Issue.15
, pp. 1819-1826
-
-
Kislyuk, A.O.1
Katz, L.S.2
Agrawal, S.3
Hagen, M.S.4
Conley, A.B.5
Jayaraman, P.6
Nelakuditi, V.7
Humphrey, J.C.8
Sammons, S.A.9
Govil, D.10
Mair, R.D.11
Tatti, K.M.12
Tondella, M.L.13
Harcourt, B.H.14
Mayer, L.W.15
Jordan, I.K.16
-
20
-
-
84901391716
-
-
Velvet Optimizer
-
Velvet Optimizer http://bioinformatics.net.au/software.velvetoptimiser.shtml, Velvet Optimizer.
-
-
-
-
21
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de bruijn graphs
-
10.1101/gr.074492.107, 2336801, 18349386
-
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de bruijn graphs. Genome Res 2008, 18(5):821-829. 10.1101/gr.074492.107, 2336801, 18349386.
-
(2008)
Genome Res
, vol.18
, Issue.5
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
22
-
-
79955724657
-
Comparing de novo genome assembly: the long and short of it
-
Narzisi G, Mishra B. Comparing de novo genome assembly: the long and short of it. PLoS One 2011, 6(4):17-17.
-
(2011)
PLoS One
, vol.6
, Issue.4
, pp. 17-17
-
-
Narzisi, G.1
Mishra, B.2
-
23
-
-
70349204183
-
Maximum likelihood genome assembly
-
10.1089/cmb.2009.0047, 3154397, 19645596
-
Medvedev P, Brudno M. Maximum likelihood genome assembly. J Comput Biol 2009, 16(8):1101-1116. 10.1089/cmb.2009.0047, 3154397, 19645596.
-
(2009)
J Comput Biol
, vol.16
, Issue.8
, pp. 1101-1116
-
-
Medvedev, P.1
Brudno, M.2
-
25
-
-
84888378526
-
An extended genovo metagenomic assembler by incorporating paired-end information
-
3817583, 24281688
-
Hayati A, Sato K, Sakakibara Y. An extended genovo metagenomic assembler by incorporating paired-end information. PeerJ 2013, 1:e196. 3817583, 24281688.
-
(2013)
PeerJ
, vol.1
-
-
Hayati, A.1
Sato, K.2
Sakakibara, Y.3
-
26
-
-
84872152255
-
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
-
10.1186/gb-2013-14-1-r2, 23320958
-
Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol 2013, 14(1):R2. 10.1186/gb-2013-14-1-r2, 23320958.
-
(2013)
Genome Biol
, vol.14
, Issue.1
-
-
Treangen, T.J.1
Koren, S.2
Sommer, D.D.3
Liu, B.4
Astrovskaya, I.5
Ondov, B.6
Darling, A.E.7
Phillippy, A.M.8
Pop, M.9
-
27
-
-
55549089660
-
Accurate whole human genome sequencing using reversible terminator chemistry
-
10.1038/nature07517, 2581791,2581791, 18987734
-
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456(7218):53-59. 10.1038/nature07517, 2581791,2581791, 18987734.
-
(2008)
Nature
, vol.456
, Issue.7218
, pp. 53-59
-
-
Bentley, D.R.1
Balasubramanian, S.2
Swerdlow, H.P.3
Smith, G.P.4
Milton, J.5
Brown, C.G.6
Hall, K.P.7
Evers, D.J.8
Barnes, C.L.9
Bignell, H.R.10
Boutell, J.M.11
Bryant, J.12
Carter, R.J.13
Keira Cheetham, R.14
Cox, A.J.15
Ellis, D.J.16
Flatbush, M.R.17
Gormley, N.A.18
Humphray, S.J.19
Irving, L.J.20
Karbelashvili, M.S.21
Kirk, S.M.22
Li, H.23
Liu, X.24
Maisinger, K.S.25
Murray, L.J.26
Obradovic, B.27
Ost, T.28
Parkinson, M.L.29
Pratt, M.R.30
more..
-
28
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
1464427, 16056220
-
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim J-B, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437(7057):376-380. 1464427, 16056220.
-
(2005)
Nature
, vol.437
, Issue.7057
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
Bemben, L.A.6
Berka, J.7
Braverman, M.S.8
Chen, Y.-J.9
Chen, Z.10
Dewell, S.B.11
Du, L.12
Fierro, J.M.13
Gomes, X.V.14
Godwin, B.C.15
He, W.16
Helgesen, S.17
Ho, C.H.18
Irzyk, G.P.19
Jando, S.C.20
Alenquer, M.L.I.21
Jarvie, T.P.22
Jirage, K.B.23
Kim, J.-B.24
Knight, J.R.25
Lanza, J.R.26
Leamon, J.H.27
Lefkowitz, S.M.28
Lei, M.29
Li, J.30
more..
-
29
-
-
79960597679
-
An integrated semiconductor device enabling non-optical genome sequencing
-
10.1038/nature10242, 21776081
-
Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011, 475(7356):348-352. 10.1038/nature10242, 21776081.
-
(2011)
Nature
, vol.475
, Issue.7356
, pp. 348-352
-
-
Rothberg, J.M.1
Hinz, W.2
Rearick, T.M.3
Schultz, J.4
Mileski, W.5
Davey, M.6
Leamon, J.H.7
Johnson, K.8
Milgrew, M.J.9
Edwards, M.10
Hoon, J.11
Simons, J.F.12
Marran, D.13
Myers, J.W.14
Davidson, J.F.15
Branting, A.16
Nobile, J.R.17
Puc, B.P.18
Light, D.19
Clark, T.A.20
Huber, M.21
Branciforte, J.T.22
Stoner, I.B.23
Cawley, S.E.24
Lyons, M.25
Fu, Y.26
Homer, N.27
Sedova, M.28
Miao, X.29
Reed, B.30
more..
-
30
-
-
58149234737
-
Real-time DNA sequencing from single polymerase molecules
-
10.1126/science.1162986, 19023044
-
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, et al. Real-time DNA sequencing from single polymerase molecules. Science 2009, 323(5910):133-138. 10.1126/science.1162986, 19023044.
-
(2009)
Science
, vol.323
, Issue.5910
, pp. 133-138
-
-
Eid, J.1
Fehr, A.2
Gray, J.3
Luong, K.4
Lyle, J.5
Otto, G.6
Peluso, P.7
Rank, D.8
Baybayan, P.9
Bettman, B.10
Bibillo, A.11
Bjornson, K.12
Chaudhuri, B.13
Christians, F.14
Cicero, R.15
Clark, S.16
Dalal, R.17
Dewinter, A.18
Dixon, J.19
Foquet, M.20
Gaertner, A.21
Hardenbol, P.22
Heiner, C.23
Hester, K.24
Holden, D.25
Kearns, G.26
Kong, X.27
Kuse, R.28
Lacroix, Y.29
Lin, S.30
more..
-
31
-
-
77958489718
-
Ruffus: a lightweight python library for computational pipelines
-
10.1093/bioinformatics/btq524, 20847218
-
Goodstadt L. Ruffus: a lightweight python library for computational pipelines. Bioinformatics 2010, 26(21):2778-2779. 10.1093/bioinformatics/btq524, 20847218.
-
(2010)
Bioinformatics
, vol.26
, Issue.21
, pp. 2778-2779
-
-
Goodstadt, L.1
-
32
-
-
84901459920
-
-
PyInstaller
-
PyInstaller http://www.pyinstaller.org/, PyInstaller.
-
-
-
-
33
-
-
66449136667
-
ABySS: a parallel assembler for short read sequence data
-
10.1101/gr.089532.108, 2694472, 19251739
-
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I. ABySS: a parallel assembler for short read sequence data. Genome Res 2009, 19(6):1117-1123. 10.1101/gr.089532.108, 2694472, 19251739.
-
(2009)
Genome Res
, vol.19
, Issue.6
, pp. 1117-1123
-
-
Simpson, J.T.1
Wong, K.2
Jackman, S.D.3
Schein, J.E.4
Jones, S.J.M.5
Birol, I.6
-
34
-
-
57249105124
-
Aggressive assembly of pyrosequencing reads with mates
-
10.1093/bioinformatics/btn548, 2639302, 18952627
-
Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 2008, 24(24):2818-2824. 10.1093/bioinformatics/btn548, 2639302, 18952627.
-
(2008)
Bioinformatics
, vol.24
, Issue.24
, pp. 2818-2824
-
-
Miller, J.R.1
Delcher, A.L.2
Koren, S.3
Venter, E.4
Walenz, B.P.5
Brownley, A.6
Johnson, J.7
Li, K.8
Mobarry, C.9
Sutton, G.10
-
35
-
-
84861760530
-
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
-
10.1093/bioinformatics/bts174, 22495754
-
Peng Y, Leung HC, Yiu SM, Chin FY. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 2012, 28(11):1420-1428. 10.1093/bioinformatics/bts174, 22495754.
-
(2012)
Bioinformatics
, vol.28
, Issue.11
, pp. 1420-1428
-
-
Peng, Y.1
Leung, H.C.2
Yiu, S.M.3
Chin, F.Y.4
-
36
-
-
84885968059
-
The MaSuRCA genome assembler
-
10.1093/bioinformatics/btt476, 23990416
-
Zimin AV, Marcais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics 2013, 29(21):2669-2677. 10.1093/bioinformatics/btt476, 23990416.
-
(2013)
Bioinformatics
, vol.29
, Issue.21
, pp. 2669-2677
-
-
Zimin, A.V.1
Marcais, G.2
Puiu, D.3
Roberts, M.4
Salzberg, S.L.5
Yorke, J.A.6
-
37
-
-
84867397631
-
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
-
10.1093/nar/gks678, 3488206, 22821567
-
Namiki T, Hachiya T, Tanaka H, Sakakibara Y. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res 2012, 40(20):e155. 10.1093/nar/gks678, 3488206, 22821567.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.20
-
-
Namiki, T.1
Hachiya, T.2
Tanaka, H.3
Sakakibara, Y.4
-
38
-
-
3042615882
-
Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs
-
10.1101/gr.1917404, 419793, 15140833
-
Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Muller WE, Wetter T, Suhai S. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 2004, 14(6):1147-1159. 10.1101/gr.1917404, 419793, 15140833.
-
(2004)
Genome Res
, vol.14
, Issue.6
, pp. 1147-1159
-
-
Chevreux, B.1
Pfisterer, T.2
Drescher, B.3
Driesel, A.J.4
Muller, W.E.5
Wetter, T.6
Suhai, S.7
-
39
-
-
78349238864
-
Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies
-
10.1089/cmb.2009.0238, 3119603, 20958248
-
Boisvert S, Laviolette F, Corbeil J. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J Comput Biol 2010, 17(11):1519-1533. 10.1089/cmb.2009.0238, 3119603, 20958248.
-
(2010)
J Comput Biol
, vol.17
, Issue.11
, pp. 1519-1533
-
-
Boisvert, S.1
Laviolette, F.2
Corbeil, J.3
-
40
-
-
84871396799
-
Ray meta: scalable de novo metagenome assembly and profiling
-
10.1186/gb-2012-13-12-r122, 23259615
-
Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J. Ray meta: scalable de novo metagenome assembly and profiling. Genome Biol 2012, 13(12):R122. 10.1186/gb-2012-13-12-r122, 23259615.
-
(2012)
Genome Biol
, vol.13
, Issue.12
-
-
Boisvert, S.1
Raymond, F.2
Godzaridis, E.3
Laviolette, F.4
Corbeil, J.5
-
41
-
-
84857838310
-
Efficient de novo assembly of large genomes using compressed data structures
-
10.1101/gr.126953.111, 3290790, 22156294
-
Simpson JT, Durbin R. Efficient de novo assembly of large genomes using compressed data structures. Genome Res 2012, 22(3):549-556. 10.1101/gr.126953.111, 3290790, 22156294.
-
(2012)
Genome Res
, vol.22
, Issue.3
, pp. 549-556
-
-
Simpson, J.T.1
Durbin, R.2
-
42
-
-
84942887758
-
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
-
10.1186/2047-217X-1-18, 3626529, 23587118
-
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 2012, 1(1):18. 10.1186/2047-217X-1-18, 3626529, 23587118.
-
(2012)
GigaScience
, vol.1
, Issue.1
, pp. 18
-
-
Luo, R.1
Liu, B.2
Xie, Y.3
Li, Z.4
Huang, W.5
Yuan, J.6
He, G.7
Chen, Y.8
Pan, Q.9
Liu, Y.10
Tang, J.11
Wu, G.12
Zhang, H.13
Shi, Y.14
Liu, Y.15
Yu, C.16
Wang, B.17
Lu, Y.18
Han, C.19
Cheung, D.W.20
Yiu, S.M.21
Peng, S.22
Xiaoqian, Z.23
Liu, G.24
Liao, X.25
Li, Y.26
Yang, H.27
Wang, J.28
Lam, T.W.29
Wang, J.30
more..
-
43
-
-
84860771820
-
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
-
10.1089/cmb.2012.0021, 3342519, 22506599
-
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012, 19(5):455-477. 10.1089/cmb.2012.0021, 3342519, 22506599.
-
(2012)
J Comput Biol
, vol.19
, Issue.5
, pp. 455-477
-
-
Bankevich, A.1
Nurk, S.2
Antipov, D.3
Gurevich, A.A.4
Dvorkin, M.5
Kulikov, A.S.6
Lesin, V.M.7
Nikolenko, S.I.8
Pham, S.9
Prjibelski, A.D.10
Pyshkin, A.V.11
Sirotkin, A.V.12
Vyahhi, N.13
Tesler, G.14
Alekseyev, M.A.15
Pevzner, P.A.16
-
44
-
-
84866712746
-
Exploiting sparseness in de novo genome assembly
-
Ye C, Ma ZS, Cannon CH, Pop M, Yu DW. Exploiting sparseness in de novo genome assembly. BMC Bioinforma 2012, 13(Suppl 6):S1.
-
(2012)
BMC Bioinforma
, vol.13
, Issue.SUPPL. 6
-
-
Ye, C.1
Ma, Z.S.2
Cannon, C.H.3
Pop, M.4
Yu, D.W.5
-
45
-
-
80054732674
-
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets
-
10.1038/nbt.1966, 3558281, 21926975
-
Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat Biotechnol 2011, 29(10):915-921. 10.1038/nbt.1966, 3558281, 21926975.
-
(2011)
Nat Biotechnol
, vol.29
, Issue.10
, pp. 915-921
-
-
Chitsaz, H.1
Yee-Greenbaum, J.L.2
Tesler, G.3
Lombardo, M.J.4
Dupont, C.L.5
Badger, J.H.6
Novotny, M.7
Rusch, D.B.8
Fraser, L.J.9
Gormley, N.A.10
Schulz-Trieglaff, O.11
Smith, G.P.12
Evers, D.J.13
Pevzner, P.A.14
Lasken, R.S.15
-
46
-
-
84891349005
-
Informed and automated k-mer size selection for genome assembly
-
10.1093/bioinformatics/btt310, 23732276
-
Chikhi R, Medvedev P. Informed and automated k-mer size selection for genome assembly. Bioinformatics 2014, 30(1):31-37. 10.1093/bioinformatics/btt310, 23732276.
-
(2014)
Bioinformatics
, vol.30
, Issue.1
, pp. 31-37
-
-
Chikhi, R.1
Medvedev, P.2
-
47
-
-
84872835269
-
Haplotype-based variant detection from short-read sequencing
-
arXiv preprint arXiv:1207.3907
-
Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. 2012, arXiv preprint arXiv:1207.3907.
-
(2012)
-
-
Garrison, E.1
Marth, G.2
-
48
-
-
58149527706
-
A genomic distance based on MUM indicates discontinuity between most bacterial species and genera
-
10.1128/JB.01202-08, 2612450, 18978054
-
Deloger M, El Karoui M, Petit MA. A genomic distance based on MUM indicates discontinuity between most bacterial species and genera. J Bacteriol 2009, 191(1):91-99. 10.1128/JB.01202-08, 2612450, 18978054.
-
(2009)
J Bacteriol
, vol.191
, Issue.1
, pp. 91-99
-
-
Deloger, M.1
El Karoui, M.2
Petit, M.A.3
-
49
-
-
84901476442
-
-
NCBI RefSeq
-
NCBI RefSeq ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz, NCBI RefSeq.
-
-
-
-
50
-
-
84901417347
-
Prokka: rapid prokaryotic genome annotation
-
btu153
-
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014, btu153.
-
(2014)
Bioinformatics
-
-
Seemann, T.1
-
51
-
-
84899090573
-
Kraken: ultrafast metagenomic sequence classification using exact alignments
-
10.1186/gb-2014-15-3-r46, 24580807
-
Wood D, Salzberg S. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 2014, 15(3):R46. 10.1186/gb-2014-15-3-r46, 24580807.
-
(2014)
Genome Biol
, vol.15
, Issue.3
-
-
Wood, D.1
Salzberg, S.2
-
52
-
-
79961139783
-
Classifying short genomic fragments from novel lineages using composition and homology
-
Parks DH, MacDonald NJ, Beiko RG. Classifying short genomic fragments from novel lineages using composition and homology. BMC Bioinforma 2011, 12(1):328-328.
-
(2011)
BMC Bioinforma
, vol.12
, Issue.1
, pp. 328-328
-
-
Parks, D.H.1
MacDonald, N.J.2
Beiko, R.G.3
-
53
-
-
84895751645
-
PhyloSift: phylogenetic analysis of genomes and metagenomes
-
3897386, 24482762
-
Darling AE, Jospin G, Lowe E, Matsen FAIV, Bik HM, Eisen JA. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2014, 2:e243. 3897386, 24482762.
-
(2014)
PeerJ
, vol.2
-
-
Darling, A.E.1
Jospin, G.2
Lowe, E.3
Matsen, F.A.I.V.4
Bik, H.M.5
Eisen, J.A.6
-
54
-
-
80055082271
-
Accelerated profile HMM searches
-
10.1371/journal.pcbi.1002195, 3197634, 22039361
-
Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol 2011, 7(10):e1002195-e1002195. 10.1371/journal.pcbi.1002195, 3197634, 22039361.
-
(2011)
PLoS Comput Biol
, vol.7
, Issue.10
-
-
Eddy, S.R.1
-
55
-
-
69549135124
-
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated markov models
-
10.1038/nmeth.1358, 2762791, 19648916
-
Brady A, Salzberg SL. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated markov models. Nat Methods 2009, 6(9):673-676. 10.1038/nmeth.1358, 2762791, 19648916.
-
(2009)
Nat Methods
, vol.6
, Issue.9
, pp. 673-676
-
-
Brady, A.1
Salzberg, S.L.2
-
56
-
-
84901478284
-
-
FastQC: A quality control tool for high throughput sequence data
-
FastQC: A quality control tool for high throughput sequence data http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, FastQC: A quality control tool for high throughput sequence data.
-
-
-
-
57
-
-
80053366291
-
Interactive metagenomic visualization in a web browser
-
Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a web browser. BMC Bioinforma 2011, 12(1):385-385.
-
(2011)
BMC Bioinforma
, vol.12
, Issue.1
, pp. 385-385
-
-
Ondov, B.D.1
Bergman, N.H.2
Phillippy, A.M.3
-
58
-
-
84901427938
-
-
Command-line tools for processing biological sequencing data
-
Command-line tools for processing biological sequencing data https://code.google.com/p/ea-utils/, Command-line tools for processing biological sequencing data.
-
-
-
-
59
-
-
84884995578
-
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans
-
10.1038/ng.2744, 3800747, 23995134
-
Comas I, Coscolla M, Luo T, Borrell S, Holt KE, Kato-Maeda M, Parkhill J, Malla B, Berg S, Thwaites G, Yeboah-Manu D, Bothamley G, Mei J, Wei L, Bentley S, Harris SR, Niemann S, Diel R, Aseffa A, Gao Q, Young D, Gagneux S. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet 2013, 45(10):1176-1182. 10.1038/ng.2744, 3800747, 23995134.
-
(2013)
Nat Genet
, vol.45
, Issue.10
, pp. 1176-1182
-
-
Comas, I.1
Coscolla, M.2
Luo, T.3
Borrell, S.4
Holt, K.E.5
Kato-Maeda, M.6
Parkhill, J.7
Malla, B.8
Berg, S.9
Thwaites, G.10
Yeboah-Manu, D.11
Bothamley, G.12
Mei, J.13
Wei, L.14
Bentley, S.15
Harris, S.R.16
Niemann, S.17
Diel, R.18
Aseffa, A.19
Gao, Q.20
Young, D.21
Gagneux, S.22
more..
-
60
-
-
0025183708
-
Basic local alignment search tool
-
10.1016/S0022-2836(05)80360-2, 2231712
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410. 10.1016/S0022-2836(05)80360-2, 2231712.
-
(1990)
J Mol Biol
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
61
-
-
84878409901
-
GAM-NGS: genomic assemblies merger for next generation sequencing
-
Vicedomini R, Vezzi F, Scalabrin S, Arvestad L, Policriti A. GAM-NGS: genomic assemblies merger for next generation sequencing. BMC Bioinforma 2013, 14(Suppl 7):S6.
-
(2013)
BMC Bioinforma
, vol.14
, Issue.SUPPL. 7
-
-
Vicedomini, R.1
Vezzi, F.2
Scalabrin, S.3
Arvestad, L.4
Policriti, A.5
-
62
-
-
84855179453
-
Graph accordance of next-generation sequence assemblies
-
10.1093/bioinformatics/btr588, 3244760, 22025481
-
Yao G, Ye L, Gao H, Minx P, Warren WC, Weinstock GM. Graph accordance of next-generation sequence assemblies. Bioinformatics 2012, 28(1):13-16. 10.1093/bioinformatics/btr588, 3244760, 22025481.
-
(2012)
Bioinformatics
, vol.28
, Issue.1
, pp. 13-16
-
-
Yao, G.1
Ye, L.2
Gao, H.3
Minx, P.4
Warren, W.C.5
Weinstock, G.M.6
-
63
-
-
33947398002
-
Minimus: a fast, lightweight genome assembler
-
Sommer DD, Delcher AL, Salzberg SL, Pop M. Minimus: a fast, lightweight genome assembler. BMC Bioinforma 2007, 8(1):64-64.
-
(2007)
BMC Bioinforma
, vol.8
, Issue.1
, pp. 64-64
-
-
Sommer, D.D.1
Delcher, A.L.2
Salzberg, S.L.3
Pop, M.4
-
64
-
-
84901467672
-
-
Perl Artistic License
-
Perl Artistic License http://dev.perl.org/licenses/artistic.html, Perl Artistic License.
-
-
-
|