fastGenoGAM

GenoGAM 2.0, a software tool that enables faster and more efficient implementation of Genome-wide generalized additive models (GenoGAM) to analyze ChIP-Seq data with flexible factorial design experiments. The previous implementation of GenoGAM had large runtime and memory requirements that made it difficult to apply to gigabase-scale genomes, such as mammalian genomes.

To overcome these limitations, GenoGAM 2.0 exploits the sparsity of the model, using the SuperLU direct solver for parameter fitting and sparse Cholesky factorization together with the sparse inverse subset algorithm for computing standard errors. This enables faster processing times, making it 2 to 3 orders of magnitude faster than the previous version. Additionally, the software uses the HDF5 library to store data efficiently on the hard drive, reducing memory footprint while keeping I/O low.

Whole-genome fits for human ChIP-seq datasets (ca. 300 million parameters) can now be obtained in less than 9 hours on a standard 60-core server, making the software more accessible and applicable for researchers working with large-scale genomic data.

Authors’ improvements in the performance of the GenoGAM framework not only open up its application to all types of organisms but also offer algorithmic improvements for fitting large GAMs that could be of interest to the statistical community beyond the genomics field.