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Old 08-08-2008, 01:31 PM   #59
spirit
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Join Date: Feb 2008
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And may I ask a question? What is the pair-end data of Illumina/Solexa data like? ZOOM now accepts two types of pair-end reads input. One is two fasta input files recording reads from two ends separately. ZOOM will automatically find the reads paired according to their name before mapping. The other is one fasta input files with two reads of a pair appearing in odd line and even line respectively. Thanks.

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Originally Posted by lh3 View Post
Another good program: ZOOM! Zillions of oligos mapped, which is online now at Bioinformatics. ZOOM resembles Eland a lot, but it further improves the spaced-seed method. I think SOLiD read mapper also uses quite a similar strategy of spaced seed, but it indexes genome, while ZOOM indexes reads like Eland.

Also, I believe ZOOM is carefully engineered. Outperforming eland with a similar algorithm is non-trivial, even given the advantages in the algorithm. I just wonder how ZOOM-C/I/P may perform. The authors did not give benchmark.
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