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Volumn 192, Issue 4, 2012, Pages 1249-1269

CloudMap: A cloud-based pipeline for analysis of mutant genome sequences

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; BIOINFORMATICS; CAENORHABDITIS ELEGANS; CLOUDMAP; COMPUTER PROGRAM; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; GENETIC VARIABILITY; GENOME; HETEROZYGOSITY; HOMOZYGOSITY; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ALIGNMENT;

EID: 84870686394     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.144204     Document Type: Article
Times cited : (211)

References (41)
  • 1
    • 84856736515 scopus 로고    scopus 로고
    • Genome sequencing reveals agronomically important loci in rice using MutMap
    • Abe, A., S. Kosugi, K. Yoshida, S. Natsume, H. Takagi et al., 2012. Genome sequencing reveals agronomically important loci in rice using MutMap. Nat. Biotechnol. 30: 174-178
    • (2012) Nat. Biotechnol , vol.30 , pp. 174-178
    • Abe, A.1    Kosugi, S.2    Yoshida, K.3    Natsume, S.4    Takagi, H.5
  • 3
    • 68349104949 scopus 로고    scopus 로고
    • MAQGene: Software to facilitate C elegans mutant genome sequence analysis
    • Bigelow, H., M. Doitsidou, S. Sarin, and O. Hobert, 2009. MAQGene: software to facilitate C. elegans mutant genome sequence analysis. Nat. Methods 6: 549
    • (2009) Nat. Methods , vol.6 , pp. 549
    • Bigelow, H.1    Doitsidou, M.2    Sarin, S.3    Hobert, O.4
  • 5
    • 84862506964 scopus 로고    scopus 로고
    • A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
    • Cingolani, P., and A. Platts, L. Wang le, M. Coon, T. Nguyen et al., 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6: 80-92
    • (2012) Fly (Austin) , vol.6 , pp. 80-92
    • Cingolani, P.1    Platts, A.2    le Wang, L.3    Coon, M.4    Nguyen, T.5
  • 8
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
    • DePristo, M. A., E. Banks, R. Poplin, K. V. Garimella, J. R. Maguire et al., 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43: 491-498
    • (2011) Nat. Genet , vol.43 , pp. 491-498
    • DePristo, M.A.1    Banks, E.2    Poplin, R.3    Garimella, K.V.4    Maguire, J.R.5
  • 9
    • 53249115177 scopus 로고    scopus 로고
    • Automated screening for mutants affecting dopaminergic-neuron specification in C elegans
    • Doitsidou, M., N. Flames, A. C. Lee, A. Boyanov, and O. Hobert, 2008. Automated screening for mutants affecting dopaminergic-neuron specification in C. elegans. Nat. Methods 5: 869-872
    • (2008) Nat. Methods , vol.5 , pp. 869-872
    • Doitsidou, M.1    Flames, N.2    Lee, A.C.3    Boyanov, A.4    Hobert, O.5
  • 10
    • 78149477199 scopus 로고    scopus 로고
    • C elegans mutant identification with a one-step wholegenome-sequencing and SNP mapping strategy
    • Doitsidou, M., R. J. Poole, S. Sarin, H. Bigelow, and O. Hobert, 2010. C. elegans mutant identification with a one-step wholegenome-sequencing and SNP mapping strategy. PLoS ONE 5: e15435
    • (2010) PLoS ONE , vol.5
    • Doitsidou, M.1    Poole, R.J.2    Sarin, S.3    Bigelow, H.4    Hobert, O.5
  • 11
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred II. Error probabilities
    • Ewing, B., and P. Green, 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186-194
    • (1998) Genome Res , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 12
    • 77955499817 scopus 로고    scopus 로고
    • Whole-genome profiling of mutagenesis in Caenorhabditis elegans
    • Flibotte, S., M. L. Edgley, I. Chaudhry, J. Taylor, S. E. Neil et al., 2010. Whole-genome profiling of mutagenesis in Caenorhabditis elegans. Genetics 185: 431-441
    • (2010) Genetics , vol.185 , pp. 431-441
    • Flibotte, S.1    Edgley, M.L.2    Chaudhry, I.3    Taylor, J.4    Neil, S.E.5
  • 13
    • 77952214725 scopus 로고    scopus 로고
    • The Groucho ortholog UNC-37interacts with the short Groucho-like protein LSY-22 to control developmental decisions in C elegans
    • Flowers, E. B., R. J. Poole, B. Tursun, E. Bashllari, I. Pe'er et al., 2010. The Groucho ortholog UNC-37interacts with the short Groucho-like protein LSY-22 to control developmental decisions in C. elegans. Development 137: 1799-1805
    • (2010) Development , vol.137 , pp. 1799-1805
    • Flowers, E.B.1    Poole, R.J.2    Tursun, B.3    Bashllari, E.4    Pe'er, I.5
  • 14
    • 84864477464 scopus 로고    scopus 로고
    • Synteny-based mapping-by-sequencing enabled by targeted enrichment
    • Galvao, V. C., K. J. Nordstrom, C. Lanz, P. Sulz, J. Mathieu et al., 2012. Synteny-based mapping-by-sequencing enabled by targeted enrichment. Plant J. 71: 517-526
    • (2012) Plant J , vol.71 , pp. 517-526
    • Galvao, V.C.1    Nordstrom, K.J.2    Lanz, C.3    Sulz, P.4    Mathieu, J.5
  • 17
    • 77749274428 scopus 로고    scopus 로고
    • The impact of whole genome sequencing on model system genetics: Get ready for the ride
    • Hobert, O., 2010. The impact of whole genome sequencing on model system genetics: get ready for the ride. Genetics 184: 317-319
    • (2010) Genetics , vol.184 , pp. 317-319
    • Hobert, O.1
  • 21
    • 21044446786 scopus 로고    scopus 로고
    • Functional genomic analysis of RNA interference in C elegans
    • Kim, J. K., H. W. Gabel, R. S. Kamath, M. Tewari, A. Pasquinelli et al., 2005. Functional genomic analysis of RNA interference in C. elegans. Science 308: 1164-1167
    • (2005) Science , vol.308 , pp. 1164-1167
    • Kim, J.K.1    Gabel, H.W.2    Kamath, R.S.3    Tewari, M.4    Pasquinelli, A.5
  • 22
    • 84869037809 scopus 로고    scopus 로고
    • The SACY-1 DEAD-box helicase links the somatic control of oocyte meiotic maturation to the sperm-to-oocyte switch and gamete maintenance in Caenorhabditis elegans
    • (in press)
    • Kim, S., J. A. Govindan, Z. J. Tu, and D. Greenstein, 2012. The SACY-1 DEAD-box helicase links the somatic control of oocyte meiotic maturation to the sperm-to-oocyte switch and gamete maintenance in Caenorhabditis elegans. Genetics (in press)
    • (2012) Genetics
    • Kim, S.1    Govindan, J.A.2    Tu, Z.J.3    Greenstein, D.4
  • 23
    • 84858651046 scopus 로고    scopus 로고
    • The pseudokinase NIPI-4 is a novel regulator of antimicrobial peptide gene expression
    • Labed, S. A., S. Omi, M. Gut, J. J. Ewbank, and N. Pujol, 2012. The pseudokinase NIPI-4 is a novel regulator of antimicrobial peptide gene expression. PLoS ONE 7: e33887
    • (2012) PLoS ONE , vol.7
    • Labed, S.A.1    Omi, S.2    Gut, M.3    Ewbank, J.J.4    Pujol, N.5
  • 24
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., C. Trapnell, M. Pop, and S. L. Salzberg, 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10: R25
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 25
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li, H., and R. Durbin, 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 26
    • 77957272611 scopus 로고    scopus 로고
    • A survey of sequence alignment algorithms for next-generation sequencing
    • Li, H., and N. Homer, 2010. A survey of sequence alignment algorithms for next-generation sequencing. Brief. Bioinform. 11: 473-483
    • (2010) Brief. Bioinform , vol.11 , pp. 473-483
    • Li, H.1    Homer, N.2
  • 27
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li, H., J. Ruan, and R. Durbin, 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18: 1851-1858
    • (2008) Genome Res , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 29
    • 70349739736 scopus 로고    scopus 로고
    • The Integrated Genome Browser: Free software for distribution and exploration of genome-scale datasets
    • Nicol, J. W., G. A. Helt, S. G. Blanchard Jr., A. Raja, and A. E. Loraine, 2009. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25: 2730-2731
    • (2009) Bioinformatics , vol.25 , pp. 2730-2731
    • Nicol, J.W.1    Helt, G.A.2    Blanchard Jr., S.G.3    Raja, A.4    Loraine, A.E.5
  • 30
    • 79956314887 scopus 로고    scopus 로고
    • Genotype and SNP calling from next-generation sequencing data
    • Nielsen, R., J. S. Paul, A. Albrechtsen, and Y. S. Song, 2011. Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12: 443-451
    • (2011) Nat. Rev. Genet , vol.12 , pp. 443-451
    • Nielsen, R.1    Paul, J.S.2    Albrechtsen, A.3    Song, Y.S.4
  • 31
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A. R., and I. M. Hall, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 32
    • 82355175168 scopus 로고    scopus 로고
    • Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping
    • Reece-Hoyes, J. S., A. Diallo, B. Lajoie, A. Kent, S. Shrestha et al., 2011. Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping. Nat. Methods 8: 1059-1064
    • (2011) Nat. Methods , vol.8 , pp. 1059-1064
    • Reece-Hoyes, J.S.1    Diallo, A.2    Lajoie, B.3    Kent, A.4    Shrestha, S.5
  • 33
    • 77955486655 scopus 로고    scopus 로고
    • Analysis of multiple ethyl methanesulfonate-mutagenized caenorhabditis elegans strains by whole-genome sequencing
    • Sarin, S., V. Bertrand, H. Bigelow, A. Boyanov, M. Doitsidou et al., 2010. Analysis of multiple ethyl methanesulfonate-mutagenized caenorhabditis elegans strains by whole-genome sequencing. Genetics 185: 417-430
    • (2010) Genetics , vol.185 , pp. 417-430
    • Sarin, S.1    Bertrand, V.2    Bigelow, H.3    Boyanov, A.4    Doitsidou, M.5
  • 34
    • 68349086946 scopus 로고    scopus 로고
    • SHOREmap: Simultaneous mapping and mutation identification by deep sequencing
    • Schneeberger, K., S. Ossowski, C. Lanz, T. Juul, A. H. Petersen et al., 2009. SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nat. Methods 6: 550-551
    • (2009) Nat. Methods , vol.6 , pp. 550-551
    • Schneeberger, K.1    Ossowski, S.2    Lanz, C.3    Juul, T.4    Petersen, A.H.5
  • 35
    • 38849199286 scopus 로고    scopus 로고
    • Widespread genetic incompatibility in C elegans maintained by balancing selection
    • Seidel, H. S., M. V. Rockman, and L. Kruglyak, 2008. Widespread genetic incompatibility in C. elegans maintained by balancing selection. Science 319: 589-594
    • (2008) Science , vol.319 , pp. 589-594
    • Seidel, H.S.1    Rockman, M.V.2    Kruglyak, L.3
  • 36
    • 79957467830 scopus 로고    scopus 로고
    • OrthoList: A compendium of C elegans genes with human orthologs
    • Shaye, D. D., and I. Greenwald, 2011. OrthoList: a compendium of C. elegans genes with human orthologs. PLoS ONE 6: e20085
    • (2011) PLoS ONE , vol.6
    • Shaye, D.D.1    Greenwald, I.2
  • 37
    • 78751703892 scopus 로고    scopus 로고
    • Direct conversion of C elegans germ cells into specific neuron types
    • Tursun, B., T. Patel, P. Kratsios, and O. Hobert, 2011. Direct conversion of C. elegans germ cells into specific neuron types. Science 331: 304-308
    • (2011) Science , vol.331 , pp. 304-308
    • Tursun, B.1    Patel, T.2    Kratsios, P.3    Hobert, O.4
  • 39
    • 23144462374 scopus 로고    scopus 로고
    • Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants
    • Wang, D., S. Kennedy, D. Conte Jr., J. K. Kim, H. W. Gabel et al., 2005. Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants. Nature 436: 593-597
    • (2005) Nature , vol.436 , pp. 593-597
    • Wang, D.1    Kennedy, S.2    Conte Jr., D.3    Kim, J.K.4    Gabel, H.W.5
  • 40
    • 79960150949 scopus 로고    scopus 로고
    • A left/right asymmetric neuronal differentiation program is controlled by the Caenorhabditis elegans lsy-27 zinc-finger transcription factor
    • Zhang, F., M. M. O'Meara, and O. Hobert, 2011. A left/right asymmetric neuronal differentiation program is controlled by the Caenorhabditis elegans lsy-27 zinc-finger transcription factor. Genetics 188: 753-759
    • (2011) Genetics , vol.188 , pp. 753-759
    • Zhang, F.1    O'Meara, M.M.2    Hobert, O.3
  • 41
    • 78751654713 scopus 로고    scopus 로고
    • A strategy for direct mapping and identification of mutations by wholegenome sequencing
    • Zuryn, S., S. Le Gras, K. Jamet, and S. Jarriault, 2010. A strategy for direct mapping and identification of mutations by wholegenome sequencing. Genetics 186: 427-430
    • (2010) Genetics , vol.186 , pp. 427-430
    • Zuryn, S.1    Le Gras, S.2    Jamet, K.3    Jarriault, S.4


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