Computational Requirements
The realignment graph is produced using a sliding-window approach with a window size of 250,000 bp. If local realignment is run with multiple passes, then each pass has its own realignment graph. While memory consumption is typically below two gigabytes for single-pass, processor loads are substantial. Realigning a human sample of approximately 50x coverage will take around 24 hours on a typical desktop machine with four physical cores. Building the realignment graph and realignment of reads are parallelized actions, such that the algorithm scales very well with the number of physical cores. Server machines exploiting 12 or more physical cores typically run three times faster than the desktop with only four cores.