RCSI: scalable similarity search in thousand(s) of genomes
Proceedings of the VLDB Endowment
FRESCO: Referential Compression of Highly Similar Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Motivation: Storing, transferring and maintaining genomic databases becomes a major challenge because of the rapid technology progress in DNA sequencing and correspondingly growing pace at which the sequencing data are being produced. Efficient compression, with support for extraction of arbitrary snippets of any sequence, is the key to maintaining those huge amounts of data. Results: We present an LZ77-style compression scheme for relative compression of multiple genomes of the same species. While the solution bears similarity to known algorithms, it offers significantly higher compression ratios at compression speed over an order of magnitude greater. In particular, 69 differentially encoded human genomes are compressed over 400 times at fast compression, or even 1000 times at slower compression (the reference genome itself needs much more space). Adding fast random access to text snippets decreases the ratio to ~300. Availability: GDC is available at http://sun.aei.polsl.pl/gdc. Contact: sebastian.deorowicz@polsl.pl Supplementary Information:Supplementary data are available at Bioinformatics online.