Non-overlapping clone pooling for high-throughput sequencing

Authors:
Reginaldo M. Kuroshu
Affiliations:
University of São Paulo, São Carlos, SP, Brazil
Venue:
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Year:
2012

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Abstract

Simultaneously sequencing multiple clones using second generation sequencers can speed up many essential clone-based sequencing methods. However, in applications such as fosmid clone sequencing and full-length cDNA sequencing it is important to create pools of clones that do not overlap on the genome for the identification of structural variations and alternatively spliced transcripts, respectively. We define the non-overlapping clone pooling problem and provide practical solutions based on optimal graph coloring and bin-packing algorithms with constant absolute worst case ratios, and further extend them to cope with repetitive mappings.