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Construction of five localized read sets per clone.

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posted on 21.02.2013, 12:26 by Andreas Sundquist, Mostafa Ronaghi, Haixu Tang, Pavel Pevzner, Serafim Batzoglou

(a) Clone read sets Ai are constructed by first defining the clone extent of each read, which is the inferred set of clones spanning the location of the read in the genome, and then for every clone Ci collecting all reads that contain Ci in their clone extent. (b) Intersection read sets Ii,j and Ii,k are constructed by finding for Ci the clones Cj and Ck that overlap Ci minimally to the left and right, and intersecting their respective inferred clone read sets. (c) Difference read sets Di,j and Di,k are constructed similarly by finding for Ci the clones Cj and Ck that overlap it maximally to the left and right, and subtracting the respective inferred clone read sets. Each read set is assembled independently with the Euler assembler during stage 1.

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