Published June 2024 | Version v4
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snakemake pipeline for Phoxinus phoxinus annotation

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Additional details

Software

Programming language
Python, Shell, Perl
Development Status
Active

References

  • Feron R, Zahm M, Cabau C, Klopp C, Roques C, Bouchez O, Eché C, Valière S, Donnadieu C, Haffray P, Bestin A, Morvezen R, Acloque H, Euclide PT, Wen M, Jouano E, Schartl M, Postlethwait JH, Schraidt C, Christie MR, Larson WA, Herpin A, Guiguen Y. Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens. Mol Ecol Resour. 2020 Mar;20(2):531-543. doi: 10.1111/1755-0998.13133. Epub 2020 Jan 27. PMID: 31903688; PMCID: PMC7050324.
  • Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. (2009). Blast+:architecture and applications. BMC bioinformatics, 10(1):421.
  • Altschul, A.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990). A basic local alignment search tool. J Mol Biol 215:403--410.
  • Gary Benson, Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Research, Volume 27, Issue 2, 1 January 1999, Pages 573–580, https://doi.org/10.1093/nar/27.2.573
  • Altschul, A.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990). A basic local alignment search tool. J Mol Biol 215:403--410.
  • Quinlan, A. R. (2014). BEDTools: the Swiss‐army tool for genome feature analysis. Current protocols in bioinformatics, 47(1):11-12.
  • Hoff, K.J., Lomsadze, A., Borodovsky, M. and Stanke, M. (2019). Whole-Genome Annotation with BRAKER. Methods Mol Biol. 1962:65-95, doi: 10.1007/978-1-4939-9173-0_5.