Is it because that if a read includes a paired-end, it is not easily to be found out by the current software? but why?
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I am not sure if your question makes much sense.Originally posted by found View PostIs it because that if a read includes a paired-end, it is not easily to be found out by the current software? but why?
(A) Yes, of course pair end alignment support is important. One can get more the double the information from paired ends -- e.g., the reads themselves plus the distance between them. Chaison & Pavner have an interesting paper in Genome Research commenting on the importance of paired ends.
(B) While I suspect some alignment programs do not have paired end support it is hardly missing from many packages. It has been around The Roche-provided 'newbler' program does pair-end assembly. The ABI-provided 'corona' program does paired-end matching to a reference. That latter is not assembly per se but then the ABI SOLiD is not designed for de-novo assembly because of the short read lengths.
Perhaps your question more revolves around assembly of very short reads?
Or perhaps your question revolves around the mis-assembly due to repeat regions?
In any case please restate your question more coherently.
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