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Old 03-03-2009, 01:20 AM   #5
jkbonfield
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Location: Cambridge, UK

Join Date: Jul 2008
Posts: 146
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Burrows-Wheeler transform is an algorithm, originally used for data compression in tools like bzip. The interest for bioinformatics is that with more recent tweaks (something called "FM Index") it can be both a compression tool and also an indexing tool.

This indexing tool is what makes it good for short-read aligners, bwa and bowtie being two such examples. Whether this method is optimal for you depends on the size of the reference genome you're comparing against.

As for why there are so many tools, well it's harder than you'd think. Sure it's easy to simply align data, but to do it for read-pair data with short indels taking into account multiple matches and computing probabilities that the sequence has been misaligned (etc) all adds up to a complex task. This has lead to a lot of competition between groups. I expect in time the number will dwindle as we get winners and losers.
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