Publications
Each tool has its own reference. If you used the Galaxy server, please also acknowledge the ELIXIR CZ infrastructure, as described on the Galaxy server page.
Which paper to cite
Cite the paper for the tool you used. A tool with no paper is marked as such.
- RepeatExplorer2
- Novák et al. 2013; Novák et al. 2020; Novák et al. 2010
- TAREAN
- Novák et al. 2017
- ChIP-Seq Mapper
- No publication yet; cite the repository.
- DANTE
- Novák et al. 2024; Neumann et al. 2019
- DANTE_LTR
- Novák et al. 2024
- DANTE_TIR
- No publication yet; cite the repository.
- TideCluster
- Gao et al. 2019; Novák et al. 2017
- CARP
- No publication yet; cite the repository.
- REXdb
- Neumann et al. 2019; Novák 2023
References
- Novák P., Hoštáková N., Neumann P., Macas J. (2024) DANTE and DANTE_LTR: lineage-centric annotation pipelines for long terminal repeat retrotransposons in plant genomes. NAR Genomics and Bioinformatics 6. doi:10.1093/nargab/lqae113
- Novák P. (2023) repeatexplorer/rexdb: v1.0. Zenodo. doi:10.5281/zenodo.10160279
- Novák P., Neumann P., Macas J. (2020) Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2. Nature Protocols 15: 3745-3776. doi:10.1038/s41596-020-0400-y
- Neumann P., Novák P., Hoštáková N., Macas J. (2019) Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Mobile DNA 10. doi:10.1186/s13100-018-0144-1
- Gao Y., Liu B., Wang Y., Xing Y. (2019) TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain. Bioinformatics 35: i200-i207. doi:10.1093/bioinformatics/btz376
- Novák P., Ávila Robledillo L., Koblížková A., Vrbová I., Neumann P., Macas J. (2017) TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Research 45: e111-e111. doi:10.1093/nar/gkx257
- Novák P., Neumann P., Pech J., Steinhaisl J., Macas J. (2013) RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics 29: 792-793. doi:10.1093/bioinformatics/btt054
- Novák P., Neumann P., Macas J. (2010) Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 11. doi:10.1186/1471-2105-11-378