TideCluster
Tandem repeats Galaxy CLI
Detects tandem repeats in genome assemblies and clusters them into families
Detects tandem repeat arrays in a genome assembly and groups them into families. Detection uses TideHunter; the arrays are then clustered by similarity so that one family is reported once rather than as many separate arrays, and consensus sequences are reconstructed with TAREAN.
Output
- A GFF3 file of tandem repeat arrays, labelled by family
- Consensus sequences per family
- An HTML report, with per-family tables
How to cite
- 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