A statistical approach to mutation detection in zebrafish with next-generation sequencing

Journal of Applied Ichthyology

Volumn 30, Issue 4, 2014, Pages 696-700

  Mackay, E W ^a   Schulte Merker, S ^a  

^a UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84904871902     PISSN: 01758659     EISSN: 14390426     Source Type: Journal    
DOI: 10.1111/jai.12528     Document Type: Article

References (10)

1. Bowen, M. E.; Henke, K.; Siegfried, K. R.; Warman, M. L.; Harris, M. P., 2012: Efficient mapping and cloning of mutations in zebrafish by low-coverage whole-genome sequencing. Genetics 190, 1017-1024.
2. Henke, K.; Bowen, M. E.; Harris, M. P., 2013: Perspectives for identification of mutations in the zebrafish: making use of next-generation sequencing technologies for forward genetic approaches. Methods 62, 185-196.
3. Leshchiner, I.; Alexa, K.; Kelsey, P.; Adzhubei, I.; Austin-Tse, C. A.; Cooney, J. D.; Anderson, H.; King, M. J.; Stottmann, R. W.; Garnaas, M. K.; Ha, S.; Drummond, I. A.; Paw, B. H.; North, T. E.; Beier, D. R.; Goessling, W.; Sunyaev, S. R., 2012: Mutation mapping and identification by whole-genome sequencing. Genome Res. 22, 1541-1548.
4. Li, H.; Durbin, R., 2009: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760.
5. McKenna, A.; Hanna, M.; Banks, E.; Sivachenko, A.; Cibulskis, K.; Kernytsky, A.; Garimella, K.; Altshuler, D.; Gabriel, S.; Daly, M.; DePristo, M. A., 2010: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303.
6. McLaren, W.; Pritchard, B.; Rios, D.; Chen, Y.; Flicek, P.; Cunningham, F., 2010: Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26, 2069-2070.
7. Miller, A. C.; Obholzer, N. D.; Shah, A. N.; Megason, S. G.; Moens, C. B., 2013: RNA-seq-based mapping and candidate identification of mutations from forward genetic screens. Genome Res. 23, 679-686.
8. Perez, F.; Granger, B. E., 2007: IPython: a system for interactive scientific computing. Comput. Sci. Eng. 9, 21-29.
9. Spoorendonk, K. M.; Peterson-Maduro, J.; Renn, J.; Trowe, T.; Kranenbarg, S.; Winkler, C.; Schulte-Merker, S., 2008: Retinoic acid and Cyp26b1 are critical regulators of osteogenesis in the axial skeleton. Development 135, 3765-3774.
10. Spoorendonk, K. M.; Hammond, C. L.; Huitema, L. F. A.; Vanoevelen, J.; Schulte-Merker, S., 2010: Zebrafish as a unique model system in bone research: the power of genetics and in vivo imaging. J. Appl. Ichthyol. 26, 219-224.