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Read alignment software tools | Hi-C data analysis

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Juicer
Desktop

Juicer

Analyzes terabase-scale Hi-C datasets. Juicer allows users without a…

Analyzes terabase-scale Hi-C datasets. Juicer allows users without a computational background to transform raw sequence data into normalized contact maps with one click. Juicer produces a hic file…

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ICE
Desktop

ICE Iterative Correction and Eigenvector decomposition

A computational pipeline that integrates a strategy to map sequencing reads…

A computational pipeline that integrates a strategy to map sequencing reads with a data-driven method for iterative correction of biases, yielding genome-wide maps of relative contact probabilities.…

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HiC-bench
Desktop

HiC-bench

Allows a comprehensive and reproducible analysis of Hi-C sequencing data.…

Allows a comprehensive and reproducible analysis of Hi-C sequencing data. HiC-bench performs complete Hi-C analysis starting with the alignment of reads (fastq files) and ending with the annotation…

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HiC-Pro
Desktop

HiC-Pro

Designs to process Hi-C data, from raw fastq files (paired-end Illumina data)…

Designs to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. The pipeline is flexible, scalable and optimized. It can operate either on a single…

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TADbit
Desktop

TADbit

Allows analysis and 3D modelling of 3C-based data. TADbit is a computational…

Allows analysis and 3D modelling of 3C-based data. TADbit is a computational framework including: (i) read quality control and design of the mapping strategy; (ii) mapping of reads to the reference…

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HIPPIE
Desktop
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HiC-inspector
Desktop

HiC-inspector

A bioinformatics pipeline for the automated analysis of data generated by…

A bioinformatics pipeline for the automated analysis of data generated by high-throughput chromatin conformation capture (HiC). The analysis workflow comprises steps of data formatting, genome…

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HiCUP
Desktop

HiCUP Hi-C User Pipeline

A tool for mapping and performing quality control on Hi-C data. HiCUP is…

A tool for mapping and performing quality control on Hi-C data. HiCUP is designed to take the raw sequence output from a HiC experiment and produce a filtered set of mapped interaction pairs,…

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