SUMMARY: The increasing availability of high-throughput sequencing technologies 
has led to thousands of human genomes having been sequenced in the past years. 
Efforts such as the 1000 Genomes Project further add to the availability of 
human genome variation data. However, to date, there is no method that can map 
reads of a newly sequenced human genome to a large collection of genomes. 
Instead, methods rely on aligning reads to a single reference genome. This leads 
to inherent biases and lower accuracy. To tackle this problem, a new alignment 
tool BWBBLE is introduced in this article. We (i) introduce a new compressed 
representation of a collection of genomes, which explicitly tackles the genomic 
variation observed at every position, and (ii) design a new alignment algorithm 
based on the Burrows-Wheeler transform that maps short reads from a newly 
sequenced genome to an arbitrary collection of two or more (up to millions of) 
genomes with high accuracy and no inherent bias to one specific genome.
AVAILABILITY: http://viq854.github.com/bwbble.