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Old 04-27-2009, 12:45 PM   #5
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Join Date: Feb 2008
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Actually there are a lot to say about paired-end mapping. This is where the accuracy of different aligners differs. The algorithms can be classified into four groups.

a) Eland-like strategy. Eland finds up to 10 equally best hits first and then check which pair (10x10 in total) is consistent. SSAHA2 uses a similar strategy, but seeing more top hits.

b) SOAP-like strategy. SOAP finds almost all the hits and then pair them. I do not know whether it may map a read to a suboptimal position if its mate is hanging around. I am sure SOAP-2.0.1 and BWA do this if necessary. You can say a) and b) are essentially the same, but only b) is useful to anchor reads in repeats.

c) MAQ-like strategy. MAQ does not find all the single-end hits first. It pairs the reads while doing the alignment. For programs indexing reads, this strategy is more effective and efficient than collecting all the single-end hits first.

d) We can map one end first and then do local alignment around the region pointed by the mapped reads. This strategy is usually combined with the previous. I believe NovoAlign/MAQ/BWA use this strategy as a complement to other strategies.

For short reads, proper pairing increases the coverage of the genome and substantially reduce false alignments.
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