Practical Indexing of Repetitive Collections Using Relative Lempel-Ziv

We introduce a simple and implementable compressed index for highly repetitive sequence collections based on Relative Lempel-Ziv (RLZ). On a collection of total size n compressed into z phrases from a reference string R[1..r] over alphabet [1..σ] and with hth order empirical entropy H
_h
(R), our index uses rH
_h
(R)+o(r log σ)+O(r+z log n) bits, and finds the occ occurrences of a pattern P[1..m] in time O((m+occ) log n). This is competitive with the only existing index based on RLZ, yet it is much simpler and easier to implement. On a 1GB collection of 80 yeast genomes, a variant of our index achieves the least space among competing structures (slightly over 0.1 bits per base) while outperforming or matching them in time (1-10 microseconds per occurrence found). Our largest variant (below 0.3 bits per base) offers the best search time (1-3 microseconds per occurrence) among all structures using space below 1 bit per base.