recoil - an algorithm for compression of extremely large datasets of dna data反冲,超大数据集的压缩算法的dna数据.pdfVIP

Yanovsky Algorithms for Molecular Biology 2011, 6:23 /content/6/1/23 RESEARCH Open Access ReCoil - an algorithm for compression of extremely large datasets of DNA data Vladimir Yanovsky Abstract The growing volume of generated DNA sequencing data makes the problem of its long term storage increasingly important. In this work we present ReCoil - an I/O efficient external memory algorithm designed for compression of very large collections of short reads DNA data. Typically each position of DNA sequence is covered by multiple reads of a short read dataset and our algorithm makes use of resulting redundancy to achieve high compression rate. While compression based on encoding mismatches between the dataset and a similar reference can yield high compression rate, good quality reference sequence may be unavailable. Instead, ReCoil’s compression is based on encoding the differences between similar or overlapping reads. As such reads may appear at large distances from each other in the dataset and since random access memory is a limited resource, ReCoil is designed to work efficiently in external memory, leveraging high bandwidth of modern hard disk drives. 1 Introduction it into smaller chunks will miss these similarities. Hence 1.1 Motivation our goal was a compression algorithm that works on the High speeds and relatively low prices of High Through- whole dataset at once, using external memory without a put Sequencing (HTS) technologies led to their wide- significant hit in performance. spread use for various kinds of applications, making it important to store high volumes of generated sequencing 1.2 Previous Work data efficiently.