MAKER2 scales to even the largest genomes. MAKER2 was used to annotate a 10 megabase section of the C. elegans genome (NGASP dataset). The algorithm was parallelized using MPI on an increasing number of CPU cores. The results demonstrate how MAKER2 scales almost linearly with CPU number (with a slope of near 1). If we project our results forward to the entire C. elegans genome (~100 megabases), MAKER2 should take under 10 hours on 32 CPUs to complete; similarly, the human genome (~3 gigabases) would require fewer than 24 hours on 400 CPUs.
Holt and Yandell BMC Bioinformatics 2011 12:491 doi:10.1186/1471-2105-12-491