#HIC JUICEBOX SOFTWARE#

In order to meet the engineering challenge of handling such massive datasets, Juicer supports the use of parallelization and hardware acceleration whenever possible, including CPU clusters, general-purpose graphics processing units (GP-GPUs), and field-programmable gate arrays (FPGAs). Juicer is closely based on the algorithms that we recently developed in order to analyze and annotate our terabase-scale Hi-C experiments ( Rao and Huntley et al., 2014). Here, we introduce Juicer, an easy-to-use, fully-automated pipeline for the processing and annotation of data from Hi-C and other contact mapping experiments.

Ensuring such compatibility can be a considerable engineering challenge.

#HIC JUICEBOX SOFTWARE#

Moreover, when designing tools that require high-performance computation, ensuring reliability and ease-of-use across software platforms and hardware instances becomes a crucial desideratum. In contrast, we recently generated 6.5 billion reads and 1.6 Tb of DNA sequence in order to create a single 3D map of the genome at kilobase resolution ( Rao and Huntley et al., 2014).Īlthough pipelines for Hi-C data analysis exist ( Lieberman-Aiden and Van Berkum et al., 2009 Schmid et al., 2015 Servant et al., 2015 Suria et al., 2015), these packages are not designed to process datasets at the terabase scale or to annotate the structural features that these maps reflect. Our original maps, derived from 30 million reads and 16 Gb of DNA sequence, described the genome at 1 megabase resolution ( Lieberman-Aiden and Van Berkum et al., 2009). The resulting maps reflect patterns of physical contact between loci, making it possible to deduce how loci are organized in 3D.Įfforts to improve the resolution of 3D maps have caused the amount of DNA sequence produced from Hi-C experiments to skyrocket. Hi-C experiments probe the three-dimensional structure of DNA and chromatin by ligating and sequencing DNA loci that are spatially proximate to one another ( Lieberman-Aiden and Van Berkum et al., 2009 Rao and Huntley et al., 2014).

Hic juicebox