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arXiv · 1604.03587

FSG: Fast String Graph Construction for De Novo Assembly of Reads Data

Paola Bonizzoni·Gianluca Della Vedova·Yuri Pirola·Marco Previtali·Raffaella Rizzi
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Abstract

The string graph for a collection of next-generation reads is a lossless data representation that is fundamental for de novo assemblers based on the overlap-layout-consensus paradigm. In this paper, we explore a novel approach to compute the string graph, based on the FM-index and Burrows-Wheeler Transform. We describe a simple algorithm that uses only the FM-index representation of the collection of reads to construct the string graph, without accessing the input reads. Our algorithm has been integrated into the SGA assembler as a standalone module to construct the string graph. The new integrated assembler has been assessed on a standard benchmark, showing that FSG is significantly faster than SGA while maintaining a moderate use of main memory, and showing practical advantages in running FSG on multiple threads.

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Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi. 2017-05-29. FSG: Fast String Graph Construction for De Novo Assembly of Reads Data. https://arxiv.org/abs/1604.03587

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