Additional preprocessing tools: flip, header, select, sample, merge. dedup handles imperfect matches, can consider additional columns. parse2 handles multiple ligation events (multi-way contacts, PORE-C and MC-3C technologies), better handles newer sequencing data. pairs file (with header) with contact coordinates and additional information, can be converted into a binned contact matrix using cooler. parse considers various ligation types and properly reports contact pairs. Pairtools - chromatin conformation capture (Hi-C and more) modular CLI tools (Python implementation and ecosystem), from the aligned sam/bam files (bwa, minimap, etc.)."Cooler: Scalable Storage for Hi-C Data and Other Genomically-Labeled Arrays" Bioinformatics, January 1, 2020 Documentation.Ībdennur, Nezar, and Leonid Mirny. pairtools - tools for low-level processing of mapped Hi-C paired reads.hic2cool - Lightweight converter between hic and cool contact matrices.hiclib - Python tools to QC, map, normalize, filter and analyze Hi-C data.Together with "pairs" text-based format, and hic, cooler is accepted by the 4D Nucleome Consortium DAC. cooler Python package for data loading, aggregation, merging, normalization (balancing), viewing, exporting data. ![]()
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