Fig. 2.

Overview of the CloudBurst algorithm. The map phase emits k-mers as keys for every k-mer in the reference, and for all non-overlapping k-mers in the reads. The shufle phase groups together the k-mers shared between the reads and the reference. The reduce phase extends the seeds into end-to-end alignments allowing for a fixed number of mismatches or indels. Here, two grey reference seeds are compared with a single read creating one alignment with two errors and one alignment with zero errors, while the black shared seed is extended to an alignment with three errors.