-
1
-
-
84855593661
-
An integrative variant analysis suite for whole exome next-generation sequencing data
-
DOI 10.1186/1471-2105-13-8
-
Challis D, Yu J, Evani US, Jackson AR, Paithankar S, Coarfa C, Milosavljevic A, Gibbs RA, Yu F. 2012. An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics 13:8 DOI 10.1186/1471-2105-13-8
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 8
-
-
Challis, D.1
Yu, J.2
Evani, U.S.3
Jackson, A.R.4
Paithankar, S.5
Coarfa, C.6
Milosavljevic, A.7
Gibbs, R.A.8
Yu, F.9
-
2
-
-
84874025843
-
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
-
DOI 10.1038/nbt.2514
-
Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G. 2013. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nature Biotechnology 31:213-219. DOI 10.1038/nbt.2514
-
(2013)
Nature Biotechnology
, vol.31
, pp. 213-219
-
-
Cibulskis, K.1
Lawrence, M.S.2
Carter, S.L.3
Sivachenko, A.4
Jaffe, D.5
Sougnez, C.6
Gabriel, S.7
Meyerson, M.8
Lander, E.S.9
Getz, G.10
-
3
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DOI 10.1038/ng.806
-
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics 43:491-498. DOI 10.1038/ng.806
-
(2011)
Nature Genetics
, vol.43
, pp. 491-498
-
-
DePristo, M.A.1
Banks, E.2
Poplin, R.3
Garimella, K.V.4
Maguire, J.R.5
Hartl, C.6
Philippakis, A.A.7
del Angel, G.8
Rivas, M.A.9
Hanna, M.10
McKenna, A.11
Fennell, T.J.12
Kernytsky, A.M.13
Sivachenko, A.Y.14
Cibulskis, K.15
Gabriel, S.B.16
Altshuler, D.17
Daly, M.J.18
-
4
-
-
84872835269
-
Haplotype-based variant detection from short-read sequencing
-
ArXiv preprint. arXiv:1207.3907
-
Garrison E, Marth G. 2012. Haplotype-based variant detection from short-read sequencing. ArXiv preprint. arXiv:1207.3907.
-
(2012)
-
-
Garrison, E.1
Marth, G.2
-
5
-
-
84903845835
-
GPU accelerated signal processing in the ion proton whole genome sequencer
-
Available at, accessed 31 March 2014
-
Gupta M, Siegel J. 2013. GPU accelerated signal processing in the ion proton whole genome sequencer. Available at http://on-demand.gputechconf.com/gtc/2013/presentations/S3229-Signal-Processing-Whole-Genome-quencer.pdf (accessed 31 March 2014).
-
(2013)
-
-
Gupta, M.1
Siegel, J.2
-
6
-
-
84903840805
-
Whole genome sequencing on donor cell leukemia in a patient with multiple myeloma identified gene mutations that may provide insights to leukemogenesis [Abstract 2414]
-
In, Atlanta, GA, Available at
-
Ho ESK, Chow HCH, Chan CTL, Luo R, Leung HCM, SiuMing Yiu, Chin FYL, Kwong YL, Leung AYH. 2012.Whole genome sequencing on donor cell leukemia in a patient with multiple myeloma identified gene mutations that may provide insights to leukemogenesis [Abstract 2414]. In: 54th ASH annual meeting and exposition. Atlanta, GA, Available at https://ash.confex. com/ash/2012/webprogram/Paper52519.html.
-
(2012)
54th ASH annual meeting and exposition
-
-
Ho, E.S.K.1
Chow, H.C.H.2
Chan, C.T.L.3
Luo, R.4
Leung, H.C.M.5
Yiu, S.M.6
Chin, F.Y.L.7
Kwong, Y.L.8
Leung, A.Y.H.9
-
7
-
-
84861729132
-
PIRS: profile-based Illumina pair-end reads simulator
-
DOI 10.1093/bioinformatics/bts187
-
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. 2012. pIRS: profile-based Illumina pair-end reads simulator. Bioinformatics 28:1533-1535. DOI 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
-
8
-
-
84903838095
-
-
Illumina, Bcl2FastQ Available at, accessed 31 March
-
Illumina. Bcl2FastQ. Available at https://support.illumina.com/downloads/bcl2fastq conversion software 184.ilmn (accessed 31 March 2014).
-
(2014)
-
-
-
9
-
-
84903840164
-
PCR-free pedigree@50x
-
Illumina, Available at, accessed 31 March 2014
-
Illumina. 2012. PCR-free pedigree@50x. Available at http://www.illumina.com/platinumgenomes/(accessed 31 March 2014).
-
(2012)
-
-
-
10
-
-
84903823725
-
-
Illumina, GVCFTools Available at, accessed 31 March 2014
-
Illumina. 2013. gVCFTools. Available at http://sites.google.com/site/gvcftools/(accessed 31 March 2014).
-
(2013)
-
-
-
11
-
-
84863229597
-
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing
-
DOI 10.1101/gr.129684.111
-
Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. 2012. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Research 22:568-576. DOI 10.1101/gr.129684.111
-
(2012)
Genome Research
, vol.22
, pp. 568-576
-
-
Koboldt, D.C.1
Zhang, Q.2
Larson, D.E.3
Shen, D.4
McLellan, M.D.5
Lin, L.6
Miller, C.A.7
Mardis, E.R.8
Ding, L.9
Wilson, R.K.10
-
12
-
-
84856565531
-
SomaticSniper: identification of somatic point mutations in whole genome sequencing data
-
DOI 10.1093/bioinformatics/btr665
-
Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis ER, Wilson RK, Ding L. 2012. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics 28:311-317. DOI 10.1093/bioinformatics/btr665
-
(2012)
Bioinformatics
, vol.28
, pp. 311-317
-
-
Larson, D.E.1
Harris, C.C.2
Chen, K.3
Koboldt, D.C.4
Abbott, T.E.5
Dooling, D.J.6
Ley, T.J.7
Mardis, E.R.8
Wilson, R.K.9
Ding, L.10
-
13
-
-
84890081976
-
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM
-
ArXiv preprint. arXiv:1303.3997
-
Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv preprint. arXiv:1303.3997.
-
(2013)
-
-
Li, H.1
-
14
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
DOI 10.1093/bioinformatics/btp324
-
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760. DOI 10.1093/bioinformatics/btp324
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
15
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
DOI 10.1093/bioinformatics/btp352
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079. DOI 10.1093/bioinformatics/btp352
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
Genome Project Data Processing, S.10
-
16
-
-
84942887758
-
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
-
DOI 10.1186/2047-217X-1-18
-
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. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18 DOI 10.1186/2047-217X-1-18
-
(2012)
Gigascience
, vol.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..
-
17
-
-
84878532952
-
SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner
-
DOI 10.1371/journal.pone.0065632
-
Luo R, Wong T, Zhu J, Liu CM, Zhu X, Wu E, Lee LK, Lin H, Zhu W, Cheung DW, Ting HF, Yiu SM, Peng S, Yu C, Li Y, Li R, Lam TW. 2013. SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner. PLoS ONE 8:e65632 DOI 10.1371/journal.pone.0065632.
-
(2013)
PLoS ONE
, vol.8
-
-
Luo, R.1
Wong, T.2
Zhu, J.3
Liu, C.M.4
Zhu, X.5
Wu, E.6
Lee, L.K.7
Lin, H.8
Zhu, W.9
Cheung, D.W.10
Ting, H.F.11
Yiu, S.M.12
Peng, S.13
Yu, C.14
Li, Y.15
Li, R.16
Lam, T.W.17
-
18
-
-
84881018840
-
Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms
-
DOI 10.1093/bioinformatics/btt314
-
Raczy C, Petrovski R, Saunders CT, Chorny I, Kruglyak S, Margulies EH, Chuang HY, Kallberg M, Kumar SA, Liao A, Little KM, Stromberg MP, Tanner SW. 2013. Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. Bioinformatics 29:2041-2043. DOI 10.1093/bioinformatics/btt314
-
(2013)
Bioinformatics
, vol.29
, pp. 2041-2043
-
-
Raczy, C.1
Petrovski, R.2
Saunders, C.T.3
Chorny, I.4
Kruglyak, S.5
Margulies, E.H.6
Chuang, H.Y.7
Kallberg, M.8
Kumar, S.A.9
Liao, A.10
Little, K.M.11
Stromberg, M.P.12
Tanner, S.W.13
-
19
-
-
84893024407
-
Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline
-
DOI 10.1186/1471-2105-15-30
-
Reid JG, Carroll A, Veeraraghavan N, Dahdouli M, Sundquist A, English A, Bainbridge M, White S, Salerno W, Buhay C, Yu F, Muzny D, Daly R, Duyk G, Gibbs RA, Boerwinkle E. 2014. Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline. BMC Bioinformatics 15:30 DOI 10.1186/1471-2105-15-30
-
(2014)
BMC Bioinformatics
, vol.15
, pp. 30
-
-
Reid, J.G.1
Carroll, A.2
Veeraraghavan, N.3
Dahdouli, M.4
Sundquist, A.5
English, A.6
Bainbridge, M.7
White, S.8
Salerno, W.9
Buhay, C.10
Yu, F.11
Muzny, D.12
Daly, R.13
Duyk, G.14
Gibbs, R.A.15
Boerwinkle, E.16
-
20
-
-
84866894408
-
Comprehensive genomic characterization of squamous cell lung cancers
-
The Cancer Genome Atlas Research Network, DOI 10.1038/nature11404
-
The Cancer Genome Atlas Research Network. 2012. Comprehensive genomic characterization of squamous cell lung cancers. Nature 489:519-525. DOI 10.1038/nature11404
-
(2012)
Nature
, vol.489
, pp. 519-525
-
-
|