Bowtie for Linux

Bowtie for Linux is an ultrafast, memory-efficient short read Aligner. It aligns short DNA sequences (reads) to the human genome at a rate of 25 million reads per hour on a typical workstation with 2 gigabytes of memory. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: 1.3 GB for the human genome. It supports alignment policies equivalent to Maq and Soap but is much FASTER: about 35x faster than Maq and over 350x faster than SOAP when aligning to the human genome. Features:Fixed all known problems with the --unfa/--unfq options: They now work properly with multiple threads. Fixed issue where sequence and quals were sometimes reversed. Fixed other issues causing spurious omission of unaligned reads. Added --maxfa/--maxfq options so that reads that don`t align due to the -m limit can be dumped separately from reads that don`t align at all. Alignment output is now guaranteed to be "deterministic" even when multiple threads are used. I.e., given the same input reads (in any order) and the same --seed, bowtie will produce the same alignments every time it is run, though not necessarily in the same order. This does not hold across different versions of Bowtie. Multiple other bug fixes.