TY - JOUR AU - Grivet, L. AU - Arruda, P. PY - 2002 DA - 2002// TI - Sugarcane genomics: depicting the complex genome of an important tropical crop JO - Curr Opin Plant Biol VL - 5 UR - https://doi.org/10.1016/S1369-5266(02)00234-0 DO - 10.1016/S1369-5266(02)00234-0 ID - Grivet2002 ER - TY - JOUR AU - Hotta, C. AU - Lembke, C. AU - Domingues, D. AU - Ochoa, E. AU - Cruz, G. Q. AU - Melotto-Passarin, D. AU - Marconi, T. AU - Santos, M. AU - Mollinari, M. AU - Margarido, G. A. PY - 2010 DA - 2010// TI - The biotechnology roadmap for sugarcane improvement JO - Trop Plant Biol VL - 3 UR - https://doi.org/10.1007/s12042-010-9050-5 DO - 10.1007/s12042-010-9050-5 ID - Hotta2010 ER - TY - JOUR AU - Vettore, A. L. AU - Silva, F. R. AU - Kemper, E. L. AU - Souza, G. M. AU - Silva, A. M. AU - Ferro, M. I. AU - Henrique-Silva, F. AU - Giglioti, E. A. AU - Lemos, M. V. AU - Coutinho, L. L. PY - 2003 DA - 2003// TI - Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1532103 DO - 10.1101/gr.1532103 ID - Vettore2003 ER - TY - JOUR AU - Souza, G. M. AU - Berges, H. AU - Bocs, S. AU - Casu, R. AU - D’Hont, A. AU - Ferreira, J. E. AU - Henry, R. AU - Ming, R. AU - Potier, B. AU - Sluys, M. -. A. PY - 2011 DA - 2011// TI - The sugarcane genome challenge: strategies for sequencing a highly complex genome JO - Trop Plant Biol VL - 4 UR - https://doi.org/10.1007/s12042-011-9079-0 DO - 10.1007/s12042-011-9079-0 ID - Souza2011 ER - TY - JOUR AU - Castleden, C. K. AU - Aoki, N. AU - Gillespie, V. J. AU - MacRae, E. A. AU - Quick, W. P. AU - Buchner, P. AU - Foyer, C. H. AU - Furbank, R. T. AU - Lunn, J. E. PY - 2004 DA - 2004// TI - Evolution and function of the sucrose-phosphate synthase gene families in wheat and other grasses JO - Plant Physiol VL - 135 UR - https://doi.org/10.1104/pp.104.042457 DO - 10.1104/pp.104.042457 ID - Castleden2004 ER - TY - JOUR AU - McIntyre, C. L. AU - Goode, M. L. AU - Cordeiro, G. AU - Bundock, P. AU - Eliott, F. AU - Henry, R. J. AU - Casu, R. E. AU - Bonnett, G. D. AU - Aitken, K. S. PY - 2015 DA - 2015// TI - Characterisation of alleles of the sucrose phosphate synthase gene family in sugarcane and their association with sugar-related traits JO - Mol Breed VL - 35 UR - https://doi.org/10.1007/s11032-015-0286-5 DO - 10.1007/s11032-015-0286-5 ID - McIntyre2015 ER - TY - JOUR AU - Sachdeva, M. AU - Mann, A. P. S. AU - Batta, S. K. PY - 2003 DA - 2003// TI - Multiple forms of soluble invertases in sugarcane juice: Kinetic and thermodynamic analysis JO - Sugar Tech VL - 5 UR - https://doi.org/10.1007/BF02943761 DO - 10.1007/BF02943761 ID - Sachdeva2003 ER - TY - JOUR AU - Carson, D. AU - Botha, F. PY - 2002 DA - 2002// TI - Genes expressed in sugarcane maturing internodal tissue JO - Plant Cell Rep VL - 20 UR - https://doi.org/10.1007/s00299-002-0444-1 DO - 10.1007/s00299-002-0444-1 ID - Carson2002 ER - TY - JOUR AU - Zhang, J. AU - Arro, J. AU - Chen, Y. AU - Ming, R. PY - 2013 DA - 2013// TI - Haplotype analysis of sucrose synthase gene family in three Saccharum species JO - BMC Genomics VL - 14 UR - https://doi.org/10.1186/1471-2164-14-S8-S1 DO - 10.1186/1471-2164-14-S8-S1 ID - Zhang2013 ER - TY - JOUR AU - Cardoso-Silva, C. B. AU - Costa, E. A. AU - Mancini, M. C. AU - Balsalobre, T. W. A. AU - Canesin, L. E. C. AU - Pinto, L. R. AU - Carneiro, M. S. AU - Garcia, A. A. F. AU - Souza, A. P. AU - Vicentini, R. PY - 2014 DA - 2014// TI - De novo assembly contrasting sugarcane varieties JO - PLoS ONE VL - 9 UR - https://doi.org/10.1371/journal.pone.0088462 DO - 10.1371/journal.pone.0088462 ID - Cardoso-Silva2014 ER - TY - JOUR AU - Park, J. W. AU - Benatti, T. R. AU - Marconi, T. AU - Yu, Q. AU - Solis-Gracia, N. AU - Mora, V. AU - Silva, J. A. PY - 2015 DA - 2015// TI - Cold responsive gene expression profiling of sugarcane and saccharum spontaneum with functional analysis of a cold inducible saccharum homolog of NOD26-like intrinsic protein to salt and water stress JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0125810 DO - 10.1371/journal.pone.0125810 ID - Park2015 ER - TY - JOUR AU - Paterson, A. AU - Bowers, J. AU - Bruggmann, R. AU - Dubchak, I. AU - Grimwood, J. AU - Gundlach, H. AU - Haberer, G. AU - Hellsten, U. AU - Mitros, T. AU - Poliakov, A. PY - 2009 DA - 2009// TI - The Sorghum bicolor genome and the diversification of grasses JO - Nature VL - 457 UR - https://doi.org/10.1038/nature07723 DO - 10.1038/nature07723 ID - Paterson2009 ER - TY - JOUR AU - Figueira, T. AU - Okura, V. AU - Rodrigues da Silva, F. AU - Jose da Silva, M. AU - Kudrna, D. AU - Ammiraju, J. AU - Talag, J. AU - Wing, R. AU - Arruda, P. PY - 2012 DA - 2012// TI - A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome JO - BMC Res Notes VL - 5 UR - https://doi.org/10.1186/1756-0500-5-185 DO - 10.1186/1756-0500-5-185 ID - Figueira2012 ER - TY - JOUR AU - Vettore, A. L. AU - Silva, F. R. AU - Kemper, E. L. AU - Arruda, P. PY - 2001 DA - 2001// TI - The libraries that made SUCEST JO - Genet Mol Biol VL - 24 UR - https://doi.org/10.1590/S1415-47572001000100002 DO - 10.1590/S1415-47572001000100002 ID - Vettore2001 ER - TY - STD TI - DFCI. 2016. ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/. Accessed 27 Feb 2016. UR - ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/ ID - ref15 ER - TY - CHAP AU - Manners, J. M. ED - Kader, J. C. ED - Delseny, M. PY - 2011 DA - 2011// TI - Functional genomics of sugarcane BT - Advances in botanical research, Vol 60 UR - https://doi.org/10.1016/B978-0-12-385851-1.00003-2 DO - 10.1016/B978-0-12-385851-1.00003-2 ID - Manners2011 ER - TY - JOUR AU - Hoang, N. V. AU - Furtado, A. AU - Botha, F. C. AU - Simmons, B. A. AU - Henry, R. J. PY - 2015 DA - 2015// TI - Potential for genetic improvement of sugarcane as a source of biomass for biofuels JO - Front Bioeng Biotechnol. VL - 3 UR - https://doi.org/10.3389/fbioe.2015.00182 DO - 10.3389/fbioe.2015.00182 ID - Hoang2015 ER - TY - JOUR AU - Vicentini, R. AU - Bem, L. E. V. AU - Sluys, M. A. AU - Nogueira, F. T. S. AU - Vincentz, M. PY - 2012 DA - 2012// TI - Gene content analysis of sugarcane public ESTs reveals thousands of missing coding-genes and an unexpected pool of grasses conserved ncRNAs JO - Trop Plant Biol VL - 5 UR - https://doi.org/10.1007/s12042-012-9103-z DO - 10.1007/s12042-012-9103-z ID - Vicentini2012 ER - TY - JOUR AU - Bernard, E. AU - Jacob, L. AU - Mairal, J. AU - Vert, J. -. P. PY - 2014 DA - 2014// TI - Efficient RNA isoform identification and quantification from RNA-Seq data with network flows JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu317 DO - 10.1093/bioinformatics/btu317 ID - Bernard2014 ER - TY - BOOK AU - Rastogi, S. PY - 2006 DA - 2006// TI - Cell and molecular biology: New age international ID - Rastogi2006 ER - TY - JOUR AU - Vicentini, R. AU - Bottcher, A. AU - Brito, M. S. AU - dos Santos, A. B. AU - Creste, S. AU - Landell, M. G. A. AU - Cesarino, I. AU - Mazzafera, P. PY - 2015 DA - 2015// TI - Large-scale transcriptome analysis of Two sugarcane genotypes contrasting for lignin content JO - PLoS ONE VL - 10 UR - https://doi.org/10.1371/journal.pone.0134909 DO - 10.1371/journal.pone.0134909 ID - Vicentini2015 ER - TY - JOUR AU - Dharshini, S. AU - Chakravarthi, M. AU - AN, J. AU - Manoj, V. M. AU - Naveenarani, M. AU - Kumar, R. AU - Meena, M. AU - Ram, B. AU - Appunu, C. PY - 2016 DA - 2016// TI - De novo sequencing and transcriptome analysis of a low temperature tolerant Saccharum spontaneum clone IND 00–1037 JO - J Biotechnol VL - 231 UR - https://doi.org/10.1016/j.jbiotec.2016.05.036 DO - 10.1016/j.jbiotec.2016.05.036 ID - Dharshini2016 ER - TY - STD TI - Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013;8(8):1494-1512. ID - ref23 ER - TY - STD TI - Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G, Gu S, Li S, et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics. 2014;30(12):1660-6. ID - ref24 ER - TY - STD TI - BC Cancer Agency. 2016 http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss. Accessed 20 Aug 2016. UR - http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss ID - ref25 ER - TY - STD TI - Duan J, Xia C, Zhao G, Jia J, Kong X. Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data. BMC Genomics. 2012;13(1):392. ID - ref26 ER - TY - STD TI - PacBio: http://www.pacb.com/smrt-science/smrt-sequencing/read-lengths/. Accessed 20 Aug 2016. UR - http://www.pacb.com/smrt-science/smrt-sequencing/read-lengths/ ID - ref27 ER - TY - JOUR AU - Abdel-Ghany, S. E. AU - Hamilton, M. AU - Jacobi, J. L. AU - Ngam, P. AU - Devitt, N. AU - Schilkey, F. AU - Ben-Hur, A. AU - Reddy, A. S. PY - 2016 DA - 2016// TI - A survey of the sorghum transcriptome using single-molecule long reads JO - Nat Commun VL - 7 UR - https://doi.org/10.1038/ncomms11706 DO - 10.1038/ncomms11706 ID - Abdel-Ghany2016 ER - TY - JOUR AU - Wang, B. AU - Tseng, E. AU - Regulski, M. AU - Clark, T. A. AU - Hon, T. AU - Jiao, Y. AU - Lu, Z. AU - Olson, A. AU - Stein, J. C. AU - Ware, D. PY - 2016 DA - 2016// TI - Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing JO - Nat Commun VL - 7 UR - https://doi.org/10.1038/ncomms11708 DO - 10.1038/ncomms11708 ID - Wang2016 ER - TY - STD TI - FastQC A Quality Control tool for High Throughput Sequence Data [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/]. Accessed 25 Jul 2016. UR - http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ID - ref30 ER - TY - JOUR AU - Pan, Q. AU - Shai, O. AU - Lee, L. J. AU - Frey, B. J. AU - Blencowe, B. J. PY - 2008 DA - 2008// TI - Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing JO - Nat Genet VL - 40 UR - https://doi.org/10.1038/ng.259 DO - 10.1038/ng.259 ID - Pan2008 ER - TY - JOUR AU - Wang, E. T. AU - Sandberg, R. AU - Luo, S. AU - Khrebtukova, I. AU - Zhang, L. AU - Mayr, C. AU - Kingsmore, S. F. AU - Schroth, G. P. AU - Burge, C. B. PY - 2008 DA - 2008// TI - Alternative isoform regulation in human tissue transcriptomes JO - Nature VL - 456 UR - https://doi.org/10.1038/nature07509 DO - 10.1038/nature07509 ID - Wang2008 ER - TY - JOUR AU - Parra, G. AU - Reymond, A. AU - Dabbouseh, N. AU - Dermitzakis, E. T. AU - Castelo, R. AU - Thomson, T. M. AU - Antonarakis, S. E. AU - Guigo, R. PY - 2006 DA - 2006// TI - Tandem chimerism as a means to increase protein complexity in the human genome JO - Genome Res VL - 16 UR - https://doi.org/10.1101/gr.4145906 DO - 10.1101/gr.4145906 ID - Parra2006 ER - TY - JOUR AU - Barbazuk, W. B. AU - Fu, Y. AU - McGinnis, K. M. PY - 2008 DA - 2008// TI - Genome-wide analyses of alternative splicing in plants: opportunities and challenges JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.053678.106 DO - 10.1101/gr.053678.106 ID - Barbazuk2008 ER - TY - JOUR AU - Yang, Y. AU - Walsh, C. E. PY - 2005 DA - 2005// TI - Spliceosome-mediated RNA trans-splicing JO - Mol Ther VL - 12 UR - https://doi.org/10.1016/j.ymthe.2005.09.006 DO - 10.1016/j.ymthe.2005.09.006 ID - Yang2005 ER - TY - JOUR AU - Reddy, A. S. AU - Marquez, Y. AU - Kalyna, M. AU - Barta, A. PY - 2013 DA - 2013// TI - Complexity of the alternative splicing landscape in plants JO - Plant Cell VL - 25 UR - https://doi.org/10.1105/tpc.113.117523 DO - 10.1105/tpc.113.117523 ID - Reddy2013 ER - TY - JOUR AU - Qiu, Y. L. AU - Palmer, J. D. PY - 2004 DA - 2004// TI - Many independent origins of trans splicing of a plant mitochondrial group II intron JO - J Mol Evol VL - 59 UR - https://doi.org/10.1007/s00239-004-2606-y DO - 10.1007/s00239-004-2606-y ID - Qiu2004 ER - TY - JOUR AU - Pereira De Souza, A. AU - Jubier, M. F. AU - Delcher, E. AU - Lancelin, D. AU - Lejeune, B. PY - 1991 DA - 1991// TI - A trans-splicing model for the expression of the tripartite nad5 gene in wheat and maize mitochondria JO - Plant Cell VL - 3 UR - https://doi.org/10.1105/tpc.3.12.1363 DO - 10.1105/tpc.3.12.1363 ID - Pereira De Souza1991 ER - TY - JOUR AU - Longevialle, A. F. AU - Meyer, E. H. AU - Andres, C. AU - Taylor, N. L. AU - Lurin, C. AU - Millar, A. H. AU - Small, I. D. PY - 2007 DA - 2007// TI - The pentatricopeptide repeat gene OTP43 is required for trans-splicing of the mitochondrial nad1 Intron 1 in Arabidopsis thaliana JO - Plant Cell VL - 19 UR - https://doi.org/10.1105/tpc.107.054841 DO - 10.1105/tpc.107.054841 ID - Longevialle2007 ER - TY - JOUR AU - Hilson, P. AU - Allemeersch, J. AU - Altmann, T. AU - Aubourg, S. AU - Avon, A. AU - Beynon, J. AU - Bhalerao, R. P. AU - Bitton, F. AU - Caboche, M. AU - Cannoot, B. PY - 2004 DA - 2004// TI - Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.2544504 DO - 10.1101/gr.2544504 ID - Hilson2004 ER - TY - STD TI - Alberts B, Bray D, Lewis J, Raff M, Roberts K, Watson J: Molecular biology of the cell, 3rd edn. Garland Science. In.: Oxford; 1994. ID - ref41 ER - TY - JOUR AU - Carninci, P. AU - Shibata, Y. AU - Hayatsu, N. AU - Sugahara, Y. AU - Shibata, K. AU - Itoh, M. AU - Konno, H. AU - Okazaki, Y. AU - Muramatsu, M. AU - Hayashizaki, Y. PY - 2000 DA - 2000// TI - Normalization and subtraction of Cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes JO - Genome Res VL - 10 UR - https://doi.org/10.1101/gr.145100 DO - 10.1101/gr.145100 ID - Carninci2000 ER - TY - JOUR AU - Au, K. F. AU - Underwood, J. G. AU - Lee, L. AU - Wong, W. H. PY - 2012 DA - 2012// TI - Improving PacBio long read accuracy by short read alignment JO - PLoS ONE VL - 7 UR - https://doi.org/10.1371/journal.pone.0046679 DO - 10.1371/journal.pone.0046679 ID - Au2012 ER - TY - JOUR AU - Chen, J. AU - Hou, K. AU - Qin, P. AU - Liu, H. AU - Yi, B. AU - Yang, W. AU - Wu, W. PY - 2014 DA - 2014// TI - RNA-Seq for gene identification and transcript profiling of three Stevia rebaudiana genotypes JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-571 DO - 10.1186/1471-2164-15-571 ID - Chen2014 ER - TY - STD TI - Nakasugi K, Crowhurst R, Bally J, Waterhouse P. Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant Nicotiana benthamiana. PLoS One. 2014;9(3):e91776. ID - ref45 ER - TY - JOUR AU - Bankar, K. G. AU - Todur, V. N. AU - Shukla, R. N. AU - Vasudevan, M. PY - 2015 DA - 2015// TI - Ameliorated de novo transcriptome assembly using Illumina paired end sequence data with Trinity Assembler JO - Genomics Data VL - 5 UR - https://doi.org/10.1016/j.gdata.2015.07.012 DO - 10.1016/j.gdata.2015.07.012 ID - Bankar2015 ER - TY - JOUR AU - Rana, S. B. AU - Zadlock, F. J. I. V. AU - Zhang, Z. AU - Murphy, W. R. AU - Bentivegna, C. S. PY - 2016 DA - 2016// TI - Comparison of de novo transcriptome assemblers and k-mer strategies using the killifish, fundulus heteroclitus JO - PLoS ONE VL - 11 UR - https://doi.org/10.1371/journal.pone.0153104 DO - 10.1371/journal.pone.0153104 ID - Rana2016 ER - TY - JOUR AU - Liu, J. AU - Wang, H. AU - Chua, N. H. PY - 2015 DA - 2015// TI - Long noncoding RNA transcriptome of plants JO - Plant Biotechnol J VL - 13 UR - https://doi.org/10.1111/pbi.12336 DO - 10.1111/pbi.12336 ID - Liu2015 ER - TY - JOUR AU - Lv, Y. AU - Liang, Z. AU - Ge, M. AU - Qi, W. AU - Zhang, T. AU - Lin, F. AU - Peng, Z. AU - Zhao, H. PY - 2016 DA - 2016// TI - Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.) JO - BMC Genomics VL - 17 ID - Lv2016 ER - TY - JOUR AU - Yandell, M. AU - Ence, D. PY - 2012 DA - 2012// TI - A beginner’s guide to eukaryotic genome annotation JO - Nat Rev Genet VL - 13 UR - https://doi.org/10.1038/nrg3174 DO - 10.1038/nrg3174 ID - Yandell2012 ER - TY - JOUR AU - Li, A. AU - Zhang, J. AU - Zhou, Z. PY - 2014 DA - 2014// TI - PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme JO - BMC Bioinformatics VL - 15 UR - https://doi.org/10.1093/bib/bbs075 DO - 10.1093/bib/bbs075 ID - Li2014 ER - TY - JOUR AU - Hoang, N. V. AU - Furtado, A. AU - Donnan, L. AU - Keeffe, E. C. AU - Botha, F. C. AU - Henry, R. J. PY - 2016 DA - 2016// TI - High-throughput profiling of the fiber and sugar composition of sugarcane biomass JO - Bioenerg Res VL - 10 UR - https://doi.org/10.1007/s12155-016-9801-8 DO - 10.1007/s12155-016-9801-8 ID - Hoang2016 ER - TY - JOUR AU - Furtado, A. PY - 2014 DA - 2014// TI - RNA extraction from developing or mature wheat seeds JO - Methods Mol Biol VL - 1099 UR - https://doi.org/10.1007/978-1-62703-715-0_4 DO - 10.1007/978-1-62703-715-0_4 ID - Furtado2014 ER - TY - JOUR AU - Zhulidov, P. A. AU - Bogdanova, E. A. AU - Shcheglov, A. S. AU - Shagina, I. A. AU - Vagner, L. L. AU - Khazpekov, G. L. AU - Kozhemiako, V. V. AU - Luk’ianov, S. A. AU - Shagin, D. A. PY - 2005 DA - 2005// TI - A method for the preparation of normalized cDNA libraries enriched with full-length sequences JO - Bioorg Khim VL - 31 ID - Zhulidov2005 ER - TY - JOUR AU - Shagin, D. A. AU - Rebrikov, D. V. AU - Kozhemyako, V. B. AU - Altshuler, I. M. AU - Shcheglov, A. S. AU - Zhulidov, P. A. AU - Bogdanova, E. A. AU - Staroverov, D. B. AU - Rasskazov, V. A. AU - Lukyanov, S. PY - 2002 DA - 2002// TI - A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.547002 DO - 10.1101/gr.547002 ID - Shagin2002 ER - TY - STD TI - Pacific Biosciences: https://github.com/PacificBiosciences/cDNA_primer/wiki/Understanding-PacBio-transcriptome-data#getFL. Accessed 15 Aug 2016. 2016. UR - https://github.com/PacificBiosciences/cDNA_primer/wiki/Understanding-PacBio-transcriptome-data#getFL ID - ref56 ER - TY - STD TI - Pacific Biosciences. 2016. https://github.com/PacificBiosciences/cDNA_primer/wiki/RS_IsoSeq-%28v2.3%29-Tutorial-%232.-Isoform-level-clustering-%28ICE-and-Quiver%29. Accessed 15 Aug 2016. UR - https://github.com/PacificBiosciences/cDNA_primer/wiki/RS_IsoSeq-%28v2.3%29-Tutorial-%232.-Isoform-level-clustering-%28ICE-and-Quiver%29 ID - ref57 ER - TY - JOUR AU - Au, K. F. AU - Sebastiano, V. AU - Afshar, P. T. AU - Durruthy, J. D. AU - Lee, L. AU - Williams, B. A. AU - Bakel, H. AU - Schadt, E. E. AU - Reijo-Pera, R. A. AU - Underwood, J. G. PY - 2013 DA - 2013// TI - Characterization of the human ESC transcriptome by hybrid sequencing JO - Proc Natl Acad Sci U S A VL - 110 UR - https://doi.org/10.1073/pnas.1320101110 DO - 10.1073/pnas.1320101110 ID - Au2013 ER - TY - JOUR AU - Hackl, T. AU - Hedrich, R. AU - Schultz, J. AU - Forster, F. PY - 2014 DA - 2014// TI - Proovread: large-scale high-accuracy PacBio correction through iterative short read consensus JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu392 DO - 10.1093/bioinformatics/btu392 ID - Hackl2014 ER - TY - JOUR AU - Salmela, L. AU - Rivals, E. PY - 2014 DA - 2014// TI - LoRDEC: accurate and efficient long read error correction JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu538 DO - 10.1093/bioinformatics/btu538 ID - Salmela2014 ER - TY - STD TI - BBMap: http://sourceforge.net/projects/bbmap/. Accessed 22 May 2016. 2016. UR - http://sourceforge.net/projects/bbmap/ ID - ref61 ER - TY - JOUR AU - He, B. AU - Zhao, S. AU - Chen, Y. AU - Cao, Q. AU - Wei, C. AU - Cheng, X. AU - Zhang, Y. PY - 2015 DA - 2015// TI - Optimal assembly strategies of transcriptome related to ploidies of eukaryotic organisms JO - BMC Genomics VL - 16 UR - https://doi.org/10.1186/1471-2164-16-1 DO - 10.1186/1471-2164-16-1 ID - He2015 ER - TY - JOUR AU - Grabherr, M. G. AU - Haas, B. J. AU - Yassour, M. AU - Levin, J. Z. AU - Thompson, D. A. AU - Amit, I. AU - Adiconis, X. AU - Fan, L. AU - Raychowdhury, R. AU - Zeng, Q. PY - 2011 DA - 2011// TI - Full-length transcriptome assembly from RNA-Seq data without a reference genome JO - Nat Biotech VL - 29 UR - https://doi.org/10.1038/nbt.1883 DO - 10.1038/nbt.1883 ID - Grabherr2011 ER - TY - JOUR AU - Schulz, M. H. AU - Zerbino, D. R. AU - Vingron, M. AU - Birney, E. PY - 2012 DA - 2012// TI - Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts094 DO - 10.1093/bioinformatics/bts094 ID - Schulz2012 ER - TY - JOUR AU - Fu, L. AU - Niu, B. AU - Zhu, Z. AU - Wu, S. AU - Li, W. PY - 2012 DA - 2012// TI - CD-HIT: accelerated for clustering the next-generation sequencing data JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts565 DO - 10.1093/bioinformatics/bts565 ID - Fu2012 ER - TY - JOUR AU - Parra, G. AU - Bradnam, K. AU - Ning, Z. AU - Keane, T. AU - Korf, I. PY - 2009 DA - 2009// TI - Assessing the gene space in draft genomes JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn916 DO - 10.1093/nar/gkn916 ID - Parra2009 ER - TY - JOUR AU - Parra, G. AU - Bradnam, K. AU - Korf, I. PY - 2007 DA - 2007// TI - CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm071 DO - 10.1093/bioinformatics/btm071 ID - Parra2007 ER - TY - JOUR AU - Simão, F. A. AU - Waterhouse, R. M. AU - Ioannidis, P. AU - Kriventseva, E. V. AU - Zdobnov, E. M. PY - 2015 DA - 2015// TI - BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv351 DO - 10.1093/bioinformatics/btv351 ID - Simão2015 ER - TY - STD TI - UniProt: http://www.uniprot.org/taxonomy/33090. Accessed 15 May 2016. 2016. UR - http://www.uniprot.org/taxonomy/33090 ID - ref69 ER - TY - STD TI - TransDecoder: https://transdecoder.github.io/. Accessed 15 May 2016. 2016. UR - https://transdecoder.github.io/ ID - ref70 ER - TY - STD TI - HMMER: http://hmmer.org/. Accessed 15 May 2016. 2016. UR - http://hmmer.org/ ID - ref71 ER - TY - CHAP AU - Gilbert, D. PY - 2013 DA - 2013// TI - Gene-omes built from mRNA seq not genome DNA BT - 7th annual arthropod genomics symposium Notre Dame: 2013 ID - Gilbert2013 ER - TY - STD TI - EvidentialGene: http://arthropods.eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html. Accessed 25 May 2016. 2016. UR - http://arthropods.eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html ID - ref73 ER - TY - STD TI - Exonerate: http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate. Accessed 25 May 2016. 2016. UR - http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate ID - ref74 ER - TY - STD TI - Smit A, Hubley R, Green P: RepeatMasker Open-4.0 2013–2015. http://www.repeatmaskerorg Accessed on 25 Mar 2015 2015. UR - http://www.repeatmaskerorg/ ID - ref75 ER - TY - STD TI - Cross_Match: http://www.phrap.org/phredphrapconsed.html. Accessed 25 May 2016. 2016. UR - http://www.phrap.org/phredphrapconsed.html ID - ref76 ER - TY - STD TI - GIRI: http://www.girinst.org/. Accessed 01 Aug 2016. 2016. UR - http://www.girinst.org/ ID - ref77 ER - TY - JOUR AU - Hubley, R. AU - Finn, R. D. AU - Clements, J. AU - Eddy, S. R. AU - Jones, T. A. AU - Bao, W. AU - Smit, A. F. A. AU - Wheeler, T. J. PY - 2016 DA - 2016// TI - The Dfam database of repetitive DNA families JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1272 DO - 10.1093/nar/gkv1272 ID - Hubley2016 ER - TY - STD TI - MISA: http://pgrc.ipk-gatersleben.de/misa/misa.html. Accessed 01 Aug 2016. 2016. UR - http://pgrc.ipk-gatersleben.de/misa/misa.html ID - ref79 ER - TY - STD TI - Phytozome: https://phytozome.jgi.doe.gov/pz/portal.html. Accessed 20 May 2016. 2016. UR - https://phytozome.jgi.doe.gov/pz/portal.html ID - ref80 ER - TY - STD TI - SUCEST-FUN Database: http://sucest-fun.org Accessed on 01 May 2015 2015. UR - http://sucest-fun.org/ ID - ref81 ER - TY - STD TI - PlantTFDB v3.0 Database: http://plntfdb.bio.uni-potsdam.de/v3.0/downloads.php. Accessed 20 May 2016. 2016. UR - http://plntfdb.bio.uni-potsdam.de/v3.0/downloads.php ID - ref82 ER - TY - STD TI - Grassius: http://grassius.org/downloads.html. Accessed 20 May 2016. 2016. UR - http://grassius.org/downloads.html ID - ref83 ER - TY - STD TI - RunIprscan: http://michaelrthon.com/runiprscan/. Accessed 20 May 2016. 2016. UR - http://michaelrthon.com/runiprscan/ ID - ref84 ER - TY - JOUR AU - Mitchell, A. AU - Chang, H. -. Y. AU - Daugherty, L. AU - Fraser, M. AU - Hunter, S. AU - Lopez, R. AU - McAnulla, C. AU - McMenamin, C. AU - Nuka, G. AU - Pesseat, S. PY - 2015 DA - 2015// TI - The InterPro protein families database: the classification resource after 15 years JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1243 DO - 10.1093/nar/gku1243 ID - Mitchell2015 ER - TY - JOUR AU - Ye, J. AU - Fang, L. AU - Zheng, H. AU - Zhang, Y. AU - Chen, J. AU - Zhang, Z. AU - Wang, J. AU - Li, S. AU - Li, R. AU - Bolund, L. PY - 2006 DA - 2006// TI - WEGO: a web tool for plotting GO annotations JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkl031 DO - 10.1093/nar/gkl031 ID - Ye2006 ER - TY - JOUR AU - Moriya, Y. AU - Itoh, M. AU - Okuda, S. AU - Yoshizawa, A. C. AU - Kanehisa, M. PY - 2007 DA - 2007// TI - KAAS: an automatic genome annotation and pathway reconstruction server JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm321 DO - 10.1093/nar/gkm321 ID - Moriya2007 ER - TY - JOUR AU - Wu, T. D. AU - Watanabe, C. K. PY - 2005 DA - 2005// TI - GMAP: a genomic mapping and alignment program for mRNA and EST sequences JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti310 DO - 10.1093/bioinformatics/bti310 ID - Wu2005 ER - TY - JOUR AU - Li, H. AU - Handsaker, B. AU - Wysoker, A. AU - Fennell, T. AU - Ruan, J. AU - Homer, N. AU - Marth, G. AU - Abecasis, G. AU - Durbin, R. PY - 2009 DA - 2009// TI - The sequence alignment/Map format and SAMtools JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 ER - TY - JOUR AU - Gurevich, A. AU - Saveliev, V. AU - Vyahhi, N. AU - Tesler, G. PY - 2013 DA - 2013// TI - QUAST: quality assessment tool for genome assemblies JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt086 DO - 10.1093/bioinformatics/btt086 ID - Gurevich2013 ER - TY - STD TI - Draw Venn Diagram: http://bioinformatics.psb.ugent.be/webtools/Venn/. Accessed 20 May 2016. UR - http://bioinformatics.psb.ugent.be/webtools/Venn/ ID - ref91 ER - TY - STD TI - Research Computing Centre. http://www.rcc.uq.edu.au. Accessed 10 Oct 2016. UR - http://www.rcc.uq.edu.au ID - ref92 ER -