a one-click pipeline for processing terabase scale Hi-C datasets. Using Juicer, you can:
Go from raw fastq files to Hi-C maps binned at many resolutions
Automatically annotate loops and contact domains with the Juicer tools
Run the pipeline in the cloud, on LSF, Univa, or SLURM, or on a single CPU
Juicer creates hic files from raw (unaligned) reads derived from a Hi-C experiment.