Mikhail D Magnitov, Veronika S Kuznetsova, Sergey V Ulianov, Sergey V Razin, Alexander V Tyakht. Benchmark of software tools for prokaryotic chromosomal interaction domain identification. Bioinformatics (2020)
Datasets used:
- Caulobacter crescentus (Le et al., Science, 2013)
- Bacillus subtilis (Wang et al., Genes Dev., 2015; Marbouty et al., Mol. Cell, 2015)
- Escherichia coli (Lioy et al., Cell, 2018)
- Mycoplasma pneumoniae (Trussart et al., Nat. Comm., 2017)
- Sulfolobus acidocaldarius (Takemata et al., Cell, 2019)
Compared domain-calling tools:
- Armatus (Filippova et al., Algorithms Mol Biol., 2014)
- Arrowhead (Durand et al., Cell Systems, 2016)
- CaTCH (Zhan et al., Genome Res., 2017)
- CHDF (Wang et al., Quant Biol, 2015)
- chromoR (Shavit and Lio, Mol. Biosyst., 2014)
- Chromosight (Matthey-Doret et al., bioRxiv, 2020)
- ClusterTAD (Oluwadare and Cheng, BMC Bioinformatics, 2017)
- deDoc (Li et al., Nat. Comm., 2018)
- Directionality Index (Dixon et al., Nature, 2012; Le et al., Science, 2013)
- EAST (Roayaei Ardakany and Lonardi, 17th International Workshop on Algorithms in Bioinformatics, 2017)
- GMAP (Yu et al., Nat. Comm., 2017)
- HiCExplorer (Ramirez et al., Nat. Comm., 2018)
- HiCseg (Levy-Leduc et al., Bioinformatics, 2014)
- IC-Finder (Haddad et al., Nucleic Acids Res., 2017)
- Insulation Score (Crane et al., Nature, 2015)
- Lavaburst
- MrTADFinder (Yan et al., PLoS Comput. Biol., 2017)
- OnTAD (An et al., Genome Biol., 2019)
- spectral (Chen et al., Bioinformatics, 2016)
- SpectralTAD (Cresswell et al., bioRxiv, 2019)
- TADbit (Serra et al., PLoS Comput. Biol., 2017)
- TADpole (Soler-Villa et al., Nucleic Acids Res., 2020)
- TADtool (Kruse et al., Bioinformatics, 2016)
- TADtree (Weinreb et al., Bioinformatics, 2015)
- TopDom (Shin et al., Nucleic Acids Res., 2016)
Available code and data:
- Hi-C and RNA-seq data processing pipelines
- Scripts to run domain callers used for benchmarking
- Annotated domain positions used in the analysis
- Scripts to analyse and validate the annotated domains
- Scripts to digest genomes and simulate Hi-C read pairs