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)

• doi: 10.1093/bioinformatics/btaa555

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