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 Hh(R), our index uses rHh(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.

MOTIVATION: Genome repositories are growing faster than our storage capacities, challenging our ability to store, transmit, process and analyze them. While genomes are not very compressible individually, those repositories usually contain myriads of genomes or genome reads of the same species, thereby creating opportunities for orders-of-magnitude compression by exploiting inter-genome similarities. A useful compression system, however, cannot be only usable for archival, but it must allow direct access to the sequences, ideally in transparent form so that applications do not need to be rewritten. RESULTS: We present a highly compressed filesystem that specializes in storing large collections of genomes and reads. The system obtains orders-of-magnitude compression by using Relative Lempel-Ziv, which exploits the high similarities between genomes of the same species. The filesystem transparently stores the files in compressed form, intervening the system calls of the applications without the need to modify them. A client/server variant of the system stores the compressed files in a server, while the client's filesystem transparently retrieves and updates the data from the server. The data between client and server are also transferred in compressed form, which saves an order of magnitude network time. AVAILABILITY AND IMPLEMENTATION: The C++ source code of our implementation is available for download in https://github.com/vsepulve/relz_fs.

Text search engines are a fundamental tool nowadays. Their efficiency relies on a popular and simple data structure: the inverted indexes. Currently, inverted indexes can be represented very efficiently using index compression schemes. Recent investigations also study how an optimized document ordering can be used to assign document identifiers (docIDs) to the document database. This yields important improvements in index compression and query processing time. In this paper we follow this line of research, yet from a different perspective. We propose a docID reassignment method that allows one to focus on a given subset of inverted lists to improve their performance. We then use run-length encoding to compress these lists (as many consecutive 1s are generated). We show that by using this approach, not only the performance of the particular subset of inverted lists is improved, but also that of the whole inverted index. Our experimental results indicate a reduction of about 10% in the space usage of the whole index docID reassignment was focused. Also, decompression speed is up to 1.22 times faster if the runs must be explicitly decompressed and up to 4.58 times faster if implicit decompression of runs is allowed. Finally, we also improve the Document-at-a-Time query processing time of AND queries (by up to 12%), WAND queries (by up to 23%) and full (non-ranked) OR queries (by up to 86%).