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This article is part of the supplement: Proceedings of the Tenth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics

Open Access Proceedings

TIGER: tiled iterative genome assembler

Xiao-Long Wu1, Yun Heo1, Izzat El Hajj1, Wen-Mei Hwu1*, Deming Chen1* and Jian Ma23*

Author Affiliations

1 Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

2 Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

3 Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

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BMC Bioinformatics 2012, 13(Suppl 19):S18  doi:10.1186/1471-2105-13-S19-S18

Published: 19 December 2012

Abstract

Background

With the cost reduction of the next-generation sequencing (NGS) technologies, genomics has provided us with an unprecedented opportunity to understand fundamental questions in biology and elucidate human diseases. De novo genome assembly is one of the most important steps to reconstruct the sequenced genome. However, most de novo assemblers require enormous amount of computational resource, which is not accessible for most research groups and medical personnel.

Results

We have developed a novel de novo assembly framework, called Tiger, which adapts to available computing resources by iteratively decomposing the assembly problem into sub-problems. Our method is also flexible to embed different assemblers for various types of target genomes. Using the sequence data from a human chromosome, our results show that Tiger can achieve much better NG50s, better genome coverage, and slightly higher errors, as compared to Velvet and SOAPdenovo, using modest amount of memory that are available in commodity computers today.

Conclusions

Most state-of-the-art assemblers that can achieve relatively high assembly quality need excessive amount of computing resource (in particular, memory) that is not available to most researchers to achieve high quality results. Tiger provides the only known viable path to utilize NGS de novo assemblers that require more memory than that is present in available computers. Evaluation results demonstrate the feasibility of getting better quality results with low memory footprint and the scalability of using distributed commodity computers.