http://seqanswers.com/forums/showthread.php?t=503&page=2
http://investor.illumina.com/phoenix.zhtml?c=121127&p=irol-newsArticle_print&ID=1248574&highlight=
Illumina refers to "paired end" as the original library preparation method they use, where you sequence each end of the same molecule. Because of the way the cluster generation technology works, it is limited to an inter-pair distance of ~300bp ( 200-600bp).
Illumina refers to "mate pairs" as sequences derived from their newer library prep method which is designed to provide paired sequences separated by a greater distance (between about 2 and 10kb). This method still actually only sequences the ends of ~400bp molecules, but this template is derived from both ends of a 2-10kb fragment that has had the middle section cut out and the 'internal' ends ligated in the middle. Basically, you take your 2-10kb random fragments, biotinylate the end, circularise them, shear the circles to ~400bp, capture biotinylated molecules, and then sequence those (they go into what is essentially a standard 'paired end' sample prep procedure).
http://www.nature.com/ng/journal/v37/n7/full/ng1562.html
http://www.nature.com/nature/journal/v431/n7011/full/nature03001.html
Used for studying structural variations
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