-
1
-
-
33751059692
-
The Marine Viromes of Four Oceanic Regions
-
Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, Chan AM, Haynes M, Kelley S, Liu H, Mahaffy JM, Mueller JE, Nulton J, Olson R, Parsons R, Rayhawk S, Suttle CA, Rohwer F: The Marine Viromes of Four Oceanic Regions. PLoS Biol 2006, 4:e368. 10.1371/journal.pbio.0040368.
-
(2006)
PLoS Biol
, vol.4
-
-
Angly, F.E.1
Felts, B.2
Breitbart, M.3
Salamon, P.4
Edwards, R.A.5
Carlson, C.6
Chan, A.M.7
Haynes, M.8
Kelley, S.9
Liu, H.10
Mahaffy, J.M.11
Mueller, J.E.12
Nulton, J.13
Olson, R.14
Parsons, R.15
Rayhawk, S.16
Suttle, C.A.17
Rohwer, F.18
-
2
-
-
34249794257
-
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
-
Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, Lapidus A, Grigoriev I, Richardson P, Hugenholtz P, Kyrpides NC: Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods 2007, 4:495-500. 10.1038/nmeth1043.
-
(2007)
Nat Methods
, vol.4
, pp. 495-500
-
-
Mavromatis, K.1
Ivanova, N.2
Barry, K.3
Shapiro, H.4
Goltsman, E.5
McHardy, A.C.6
Rigoutsos, I.7
Salamov, A.8
Korzeniewski, F.9
Land, M.10
Lapidus, A.11
Grigoriev, I.12
Richardson, P.13
Hugenholtz, P.14
Kyrpides, N.C.15
-
3
-
-
79956366297
-
Evaluating the fidelity of de novo short read metagenomic assembly using simulated data
-
Pignatelli M, Moya A: Evaluating the fidelity of de novo short read metagenomic assembly using simulated data. PLoS One 2011, 6:23.
-
(2011)
PLoS One
, vol.6
, pp. 23
-
-
Pignatelli, M.1
Moya, A.2
-
4
-
-
79960872039
-
Evaluation of short read metagenomic assembly
-
Charuvaka A, Rangwala H: Evaluation of short read metagenomic assembly. BMC Genomics 2011, 12:1471-2164.
-
(2011)
BMC Genomics
, vol.12
, pp. 1471-2164
-
-
Charuvaka, A.1
Rangwala, H.2
-
5
-
-
84857524013
-
Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
-
Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J, Bork P: Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data. PLoS One 2012, 7:e31386. 10.1371/journal.pone.0031386.
-
(2012)
PLoS One
, vol.7
-
-
Mende, D.R.1
Waller, A.S.2
Sunagawa, S.3
Järvelin, A.I.4
Chan, M.M.5
Arumugam, M.6
Raes, J.7
Bork, P.8
-
6
-
-
84856770811
-
Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample
-
Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT: Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One 2012, 7:10.
-
(2012)
PLoS One
, vol.7
, pp. 10
-
-
Luo, C.1
Tsementzi, D.2
Kyrpides, N.3
Read, T.4
Konstantinidis, K.T.5
-
7
-
-
84858863014
-
Individual genome assembly from complex community short-read metagenomic datasets
-
Luo C, Tsementzi D, Kyrpides NC, Konstantinidis KT: Individual genome assembly from complex community short-read metagenomic datasets. ISME J 2012, 6:898-901. 10.1038/ismej.2011.147.
-
(2012)
ISME J
, vol.6
, pp. 898-901
-
-
Luo, C.1
Tsementzi, D.2
Kyrpides, N.C.3
Konstantinidis, K.T.4
-
8
-
-
84892457697
-
Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut
-
Vazquez-Castellanos JF, Garcia-Lopez R, Perez-Brocal V, Pignatelli M, Moya A: Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut. BMC Genomics 2014, 15:1471-2164.
-
(2014)
BMC Genomics
, vol.15
, pp. 1471-2164
-
-
Vazquez-Castellanos, J.F.1
Garcia-Lopez, R.2
Perez-Brocal, V.3
Pignatelli, M.4
Moya, A.5
-
9
-
-
84877278609
-
Sequencing platform and library preparation choices impact viral metagenomes
-
Solonenko S, Ignacio-Espinoza J, Alberti A, Cruaud C, Hallam S, Konstantinidis K, Tyson G, Wincker P, Sullivan M: Sequencing platform and library preparation choices impact viral metagenomes. BMC Genomics 2013, 14:320. 10.1186/1471-2164-14-320.
-
(2013)
BMC Genomics
, vol.14
, pp. 320
-
-
Solonenko, S.1
Ignacio-Espinoza, J.2
Alberti, A.3
Cruaud, C.4
Hallam, S.5
Konstantinidis, K.6
Tyson, G.7
Wincker, P.8
Sullivan, M.9
-
10
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar RC: Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26:2460-2461. 10.1093/bioinformatics/btq461.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
11
-
-
77954627922
-
Viruses in the faecal microbiota of monozygotic twins and their mothers
-
Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, Gordon JI: Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 2010, 466:334-338. 10.1038/nature09199.
-
(2010)
Nature
, vol.466
, pp. 334-338
-
-
Reyes, A.1
Haynes, M.2
Hanson, N.3
Angly, F.E.4
Heath, A.C.5
Rohwer, F.6
Gordon, J.I.7
-
12
-
-
80054911634
-
Metavir: a web server dedicated to virome analysis
-
Roux S, Faubladier M, Mahul A, Paulhe N, Bernard A, Debroas D, Enault F: Metavir: a web server dedicated to virome analysis. Bioinformatics 2011, 27:3074-3075. 10.1093/bioinformatics/btr519.
-
(2011)
Bioinformatics
, vol.27
, pp. 3074-3075
-
-
Roux, S.1
Faubladier, M.2
Mahul, A.3
Paulhe, N.4
Bernard, A.5
Debroas, D.6
Enault, F.7
-
13
-
-
19144363310
-
PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information
-
Angly F, Rodriguez-Brito B, Bangor D, McNairnie P, Breitbart M, Salamon P, Felts B, Nulton J, Mahaffy J, Rohwer F: PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics 2005, 6:41. 10.1186/1471-2105-6-41.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 41
-
-
Angly, F.1
Rodriguez-Brito, B.2
Bangor, D.3
McNairnie, P.4
Breitbart, M.5
Salamon, P.6
Felts, B.7
Nulton, J.8
Mahaffy, J.9
Rohwer, F.10
-
14
-
-
84892842003
-
Estimation of viral richness from shotgun metagenomes using a frequency count approach
-
Allen HK, Bunge J, Foster JA, Bayles DO, Stanton TB: Estimation of viral richness from shotgun metagenomes using a frequency count approach. Microbiome 2013, 1:2049-2618.
-
(2013)
Microbiome
, vol.1
, pp. 2049-2618
-
-
Allen, H.K.1
Bunge, J.2
Foster, J.A.3
Bayles, D.O.4
Stanton, T.B.5
-
15
-
-
84859231246
-
Estimating population diversity with CatchAll
-
Bunge J, Woodard L, Böhning D, Foster JA, Connolly S, Allen HK: Estimating population diversity with CatchAll. Bioinformatics 2012, 28:1045-1047. 10.1093/bioinformatics/bts075.
-
(2012)
Bioinformatics
, vol.28
, pp. 1045-1047
-
-
Bunge, J.1
Woodard, L.2
Böhning, D.3
Foster, J.A.4
Connolly, S.5
Allen, H.K.6
-
16
-
-
84874194145
-
Sequence assembly demystified
-
Nagarajan N, Pop M: Sequence assembly demystified. Nat Rev Genet 2013, 14:157-167. 10.1038/nrg3367.
-
(2013)
Nat Rev Genet
, vol.14
, pp. 157-167
-
-
Nagarajan, N.1
Pop, M.2
-
17
-
-
84861729132
-
pIRS: Profile-based Illumina pair-end reads simulator
-
Hu X, Yuan J, Shi Y, Lu J, Liu B, Li Z, Chen Y, Mu D, Zhang H, Li N, Yue Z, Bai F, Li H, Fan W: pIRS: Profile-based Illumina pair-end reads simulator. Bioinformatics 2012, 28:1533-1535. 10.1093/bioinformatics/bts187.
-
(2012)
Bioinformatics
, vol.28
, pp. 1533-1535
-
-
Hu, X.1
Yuan, J.2
Shi, Y.3
Lu, J.4
Liu, B.5
Li, Z.6
Chen, Y.7
Mu, D.8
Zhang, H.9
Li, N.10
Yue, Z.11
Bai, F.12
Li, H.13
Fan, W.14
-
18
-
-
79960878783
-
Inferring viral quasispecies spectra from 454 pyrosequencing reads
-
Astrovskaya I, Tork B, Mangul S, Westbrooks K, Mandoiu I, Balfe P, Zelikovsky A: Inferring viral quasispecies spectra from 454 pyrosequencing reads. BMC Bioinformatics 2011, 12 Supp 6:S1.
-
(2011)
BMC Bioinformatics
, Issue.12
, pp. S1
-
-
Astrovskaya, I.1
Tork, B.2
Mangul, S.3
Westbrooks, K.4
Mandoiu, I.5
Balfe, P.6
Zelikovsky, A.7
-
19
-
-
77950840976
-
Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction
-
Zagordi O, Geyrhofer L, Roth V, Beerenwinkel N: Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction. J Comput Biol 2010, 17:417-428. 10.1089/cmb.2009.0164.
-
(2010)
J Comput Biol
, vol.17
, pp. 417-428
-
-
Zagordi, O.1
Geyrhofer, L.2
Roth, V.3
Beerenwinkel, N.4
-
20
-
-
34447543156
-
Power law rank-abundance models for marine phage communities
-
Hoffmann KH, Rodriguez-Brito B, Breitbart M, Bangor D, Angly F, Felts B, Nulton J, Rohwer F, Salamon P: Power law rank-abundance models for marine phage communities. FEMS Microbiol Lett 2007, 273:224-228. 10.1111/j.1574-6968.2007.00790.x.
-
(2007)
FEMS Microbiol Lett
, vol.273
, pp. 224-228
-
-
Hoffmann, K.H.1
Rodriguez-Brito, B.2
Breitbart, M.3
Bangor, D.4
Angly, F.5
Felts, B.6
Nulton, J.7
Rohwer, F.8
Salamon, P.9
-
21
-
-
84856988681
-
GemSIM: general, error-model based simulator of next-generation sequencing data
-
McElroy K, Luciani F, Thomas T: GemSIM: general, error-model based simulator of next-generation sequencing data. BMC Genomics 2012, 13:74. 10.1186/1471-2164-13-74.
-
(2012)
BMC Genomics
, vol.13
, pp. 74
-
-
McElroy, K.1
Luciani, F.2
Thomas, T.3
-
22
-
-
80455126001
-
Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems
-
Minoche A, Dohm J, Himmelbauer H: Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems. Genome Biol 2011, 12:R112. 10.1186/gb-2011-12-11-r112.
-
(2011)
Genome Biol
, vol.12
, pp. R112
-
-
Minoche, A.1
Dohm, J.2
Himmelbauer, H.3
-
23
-
-
80051688000
-
Field guide to next-generation DNA sequencers
-
Glenn TC: Field guide to next-generation DNA sequencers. Mol Ecol Resour 2011, 11:759-769. 10.1111/j.1755-0998.2011.03024.x.
-
(2011)
Mol Ecol Resour
, vol.11
, pp. 759-769
-
-
Glenn, T.C.1
-
24
-
-
54949137701
-
MetaSim-A Sequencing Simulator for Genomics and Metagenomics
-
Richter DC, Ott F, Auch AF, Schmid R, Huson DH: MetaSim-A Sequencing Simulator for Genomics and Metagenomics. PLoS One 2008, 3:e3373. 10.1371/journal.pone.0003373.
-
(2008)
PLoS One
, vol.3
-
-
Richter, D.C.1
Ott, F.2
Auch, A.F.3
Schmid, R.4
Huson, D.H.5
-
26
-
-
70449376998
-
High diversity of the viral community from an Antarctic lake
-
Lopez-Bueno A, Tamames J, Velazquez D, Moya A, Quesada A, Alcami A: High diversity of the viral community from an Antarctic lake. Science 2009, 326:858-861. 10.1126/science.1179287.
-
(2009)
Science
, vol.326
, pp. 858-861
-
-
Lopez-Bueno, A.1
Tamames, J.2
Velazquez, D.3
Moya, A.4
Quesada, A.5
Alcami, A.6
-
27
-
-
79952422304
-
Quality control and preprocessing of metagenomic datasets
-
Schmieder R, Edwards R: Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011, 27:863-864. 10.1093/bioinformatics/btr026.
-
(2011)
Bioinformatics
, vol.27
, pp. 863-864
-
-
Schmieder, R.1
Edwards, R.2
-
28
-
-
33947215475
-
CAMERA: A Community Resource for Metagenomics
-
Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M: CAMERA: A Community Resource for Metagenomics. PLoS Biol 2007, 5:e75. 10.1371/journal.pbio.0050075.
-
(2007)
PLoS Biol
, vol.5
-
-
Seshadri, R.1
Kravitz, S.A.2
Smarr, L.3
Gilna, P.4
Frazier, M.5
-
29
-
-
84861760530
-
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
-
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, 28:1420-1428. 10.1093/bioinformatics/bts174.
-
(2012)
Bioinformatics
, vol.28
, pp. 1420-1428
-
-
Peng, Y.1
Leung, H.C.2
Yiu, S.M.3
Chin, F.Y.4
-
30
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL: Versatile and open software for comparing large genomes. Genome Biol 2004, 5:30. 10.1186/gb-2004-5-5-r30.
-
(2004)
Genome Biol
, vol.5
, pp. 30
-
-
Kurtz, S.1
Phillippy, A.2
Delcher, A.L.3
Smoot, M.4
Shumway, M.5
Antonescu, C.6
Salzberg, S.L.7
-
31
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9:357-359. 10.1038/nmeth.1923.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
32
-
-
37649024043
-
The ade4 package: implementing the duality diagram for ecologists
-
Dray S: The ade4 package: implementing the duality diagram for ecologists. J Stat Softw 2007, 22:1.
-
(2007)
J Stat Softw
, vol.22
, pp. 1
-
-
Dray, S.1
-
33
-
-
13444306641
-
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
-
Pruitt KD, Tatusova T, Maglott DR: NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2005, 33:D501-D504. 10.1093/nar/gki476.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. D501-D504
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
34
-
-
84863190624
-
Grinder: a versatile amplicon and shotgun sequence simulator
-
Angly FE, Willner D, Rohwer F, Hugenholtz P, Tyson GW: Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic Acids Res 2012, 40:e94. 10.1093/nar/gks251.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Angly, F.E.1
Willner, D.2
Rohwer, F.3
Hugenholtz, P.4
Tyson, G.W.5
-
35
-
-
80051972336
-
Next generation sequence assembly with AMOS
-
Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M: Next generation sequence assembly with AMOS. Curr Protoc Bioinformatics 2011, 11:11-18.
-
(2011)
Curr Protoc Bioinformatics
, vol.11
, pp. 11-18
-
-
Treangen, T.J.1
Sommer, D.D.2
Angly, F.E.3
Koren, S.4
Pop, M.5
|