Algorithms

Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform

MOTIVATION: The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being widely …

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

The introduction of next-generation sequencing techniques and especially the high-throughput systems Solexa (Illumina Inc.) and SOLiD (ABI) made the mapping of short reads to reference sequences a standard application in modern bioinformatics. …