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Bioinformatics Advance Access originally published online on April 1, 2004
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Bioinformatics 20(13) © Oxford University Press 2004; all rights reserved.

Fragment assembly with short reads

Mark Chaisson 1,*, Pavel Pevzner 2 and Haixu Tang 2

1 Bioinformatics Program and 2 Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA

Received on October 8, 2003; revised on February 3, 2004; accepted on February 9, 2004
Advance Access Publication April 1, 2004

Motivation: Current DNA sequencing technology produces reads of about 500–750 bp, with typical coverage under 10x. New sequencing technologies are emerging that produce shorter reads (length 80–200 bp) but allow one to generate significantly higher coverage (30x and higher) at low cost. Modern assembly programs and error correction routines have been tuned to work well with current read technology but were not designed for assembly of short reads.

Results: We analyze the limitations of assembling reads generated by these new technologies and present a routine for base-calling in reads prior to their assembly. We demonstrate that while it is feasible to assemble such short reads, the resulting contigs will require significant (if not prohibitive) finishing efforts.

Availability: Available from the web at http://www.cse.ucsd.edu/groups/bioinformatics/software.html

Contact: mchaisso{at}bioinf.ucsd.edu; ppevzner{at}cs.ucsd.edu; htangg{at}cs.ucsd.edu

* To whom correspondence should be addressed.


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