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Open Access Highly Accessed Methodology article

Readjoiner: a fast and memory efficient string graph-based sequence assembler

Giorgio Gonnella and Stefan Kurtz*

Author Affiliations

Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146, Hamburg, Germany

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BMC Bioinformatics 2012, 13:82  doi:10.1186/1471-2105-13-82

Published: 6 May 2012

Additional files

Additional file 1:

Supplemental Material. This document describes implementation techniques for the methods and algorithms described in the main document. Moreover, it gives a lemma and a theorem (including proofs) characterizing transitive SPMs, and an algorithm to enumerate irreducible and non-redundant suffix-prefix matches. Furthermore, a method to recognize internally contained reads is given, as well as results for a benchmark set with reads of variable length. Finally, an example of SPM-relevant suffixes and their corresponding lcp-interval is presented.

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