Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts
Celis JS, Wibberg D, Ramírez-Portilla C, Rupp O, Sczyrba A, Winkler A, Kalinowski J, Wilke T (2018)
GigaScience 7(7): giy075.
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Autor*in
Celis, Juan Sebastián;
Wibberg, DanielUniBi;
Ramírez-Portilla, Catalina;
Rupp, Oliver;
Sczyrba, AlexanderUniBi
;
Winkler, AnikaUniBi;
Kalinowski, JörnUniBi;
Wilke, Thomas
![](https://pub.uni-bielefeld.de/images/icon_orcid.png)
Einrichtung
Erscheinungsjahr
2018
Zeitschriftentitel
GigaScience
Band
7
Ausgabe
7
Art.-Nr.
giy075
Urheberrecht / Lizenzen
ISSN
2047-217x
eISSN
2047-217X
Page URI
https://pub.uni-bielefeld.de/record/2920777
Zitieren
Celis JS, Wibberg D, Ramírez-Portilla C, et al. Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts. GigaScience. 2018;7(7): giy075.
Celis, J. S., Wibberg, D., Ramírez-Portilla, C., Rupp, O., Sczyrba, A., Winkler, A., Kalinowski, J., et al. (2018). Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts. GigaScience, 7(7), giy075. doi:10.1093/gigascience/giy075
Celis, Juan Sebastián, Wibberg, Daniel, Ramírez-Portilla, Catalina, Rupp, Oliver, Sczyrba, Alexander, Winkler, Anika, Kalinowski, Jörn, and Wilke, Thomas. 2018. “Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts”. GigaScience 7 (7): giy075.
Celis, J. S., Wibberg, D., Ramírez-Portilla, C., Rupp, O., Sczyrba, A., Winkler, A., Kalinowski, J., and Wilke, T. (2018). Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts. GigaScience 7:giy075.
Celis, J.S., et al., 2018. Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts. GigaScience, 7(7): giy075.
J.S. Celis, et al., “Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts”, GigaScience, vol. 7, 2018, : giy075.
Celis, J.S., Wibberg, D., Ramírez-Portilla, C., Rupp, O., Sczyrba, A., Winkler, A., Kalinowski, J., Wilke, T.: Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts. GigaScience. 7, : giy075 (2018).
Celis, Juan Sebastián, Wibberg, Daniel, Ramírez-Portilla, Catalina, Rupp, Oliver, Sczyrba, Alexander, Winkler, Anika, Kalinowski, Jörn, and Wilke, Thomas. “Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts”. GigaScience 7.7 (2018): giy075.
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Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J., Genome Biol. 13(12), 2012
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Fast gapped-read alignment with Bowtie 2.
Langmead B, Salzberg SL., Nat. Methods 9(4), 2012
PMID: 22388286
Langmead B, Salzberg SL., Nat. Methods 9(4), 2012
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BamTools: a C++ API and toolkit for analyzing and managing BAM files.
Barnett DW, Garrison EK, Quinlan AR, Stromberg MP, Marth GT., Bioinformatics 27(12), 2011
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Barnett DW, Garrison EK, Quinlan AR, Stromberg MP, Marth GT., Bioinformatics 27(12), 2011
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Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm.
Lomsadze A, Burns PD, Borodovsky M., Nucleic Acids Res. 42(15), 2014
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Lomsadze A, Burns PD, Borodovsky M., Nucleic Acids Res. 42(15), 2014
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Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines.
Rupp O, Becker J, Brinkrolf K, Timmermann C, Borth N, Puhler A, Noll T, Goesmann A., PLoS ONE 9(1), 2014
PMID: 24427317
Rupp O, Becker J, Brinkrolf K, Timmermann C, Borth N, Puhler A, Noll T, Goesmann A., PLoS ONE 9(1), 2014
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BEDTools: a flexible suite of utilities for comparing genomic features.
Quinlan AR, Hall IM., Bioinformatics 26(6), 2010
PMID: 20110278
Quinlan AR, Hall IM., Bioinformatics 26(6), 2010
PMID: 20110278
InterProScan 5: genome-scale protein function classification.
Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S., Bioinformatics 30(9), 2014
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Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S., Bioinformatics 30(9), 2014
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The Rhizoctonia solani AG1-IB (isolate 7/3/14) transcriptome during interaction with the host plant lettuce (Lactuca sativa L.).
Verwaaijen B, Wibberg D, Krober M, Winkler A, Zrenner R, Bednarz H, Niehaus K, Grosch R, Puhler A, Schluter A., PLoS ONE 12(5), 2017
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AUTHOR UNKNOWN, 0
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL., Genome Biol. 14(4), 2013
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Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL., Genome Biol. 14(4), 2013
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ReadXplorer--visualization and analysis of mapped sequences.
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A., Bioinformatics 30(16), 2014
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Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A., Bioinformatics 30(16), 2014
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ReadXplorer 2-detailed read mapping analysis and visualization from one single source.
Hilker R, Stadermann KB, Schwengers O, Anisiforov E, Jaenicke S, Weisshaar B, Zimmermann T, Goesmann A., Bioinformatics 32(24), 2016
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Hilker R, Stadermann KB, Schwengers O, Anisiforov E, Jaenicke S, Weisshaar B, Zimmermann T, Goesmann A., Bioinformatics 32(24), 2016
PMID: 27540267
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.
Marcais G, Kingsford C., Bioinformatics 27(6), 2011
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Marcais G, Kingsford C., Bioinformatics 27(6), 2011
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Eukaryotic genome size databases
Gregory TR, Nicol JA, Tamm H., 2007
Gregory TR, Nicol JA, Tamm H., 2007
Estimating the repeat structure and length of DNA sequences using L-tuples.
Li X, Waterman MS., Genome Res. 13(8), 2003
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Li X, Waterman MS., Genome Res. 13(8), 2003
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QUAST: quality assessment tool for genome assemblies.
Gurevich A, Saveliev V, Vyahhi N, Tesler G., Bioinformatics 29(8), 2013
PMID: 23422339
Gurevich A, Saveliev V, Vyahhi N, Tesler G., Bioinformatics 29(8), 2013
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM., Bioinformatics 31(19), 2015
PMID: 26059717
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM., Bioinformatics 31(19), 2015
PMID: 26059717
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
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Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
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Ensembl 2016
Yates A, Akanni W, Ridwan Amode M., 2016
Yates A, Akanni W, Ridwan Amode M., 2016
Genome-wide SNP analysis explains coral diversity and recovery in the Ryukyu Archipelago
Shinzato C, Mungpakdee S, Arakaki N., 2015
Shinzato C, Mungpakdee S, Arakaki N., 2015
Supporting data for “Binning Enables Efficient Host Genome Reconstruction in Cnidarian Holobionts.”
Celis JS, Wibberg D, Ramírez-Portilla C., 2018
Celis JS, Wibberg D, Ramírez-Portilla C., 2018
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