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Bioinformatics. 2010 Jul 15;26(14):1699-703. doi: 10.1093/bioinformatics/btq268. Epub 2010 May 30.

Gap5--editing the billion fragment sequence assembly.

Author information

1
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK. jkb@sanger.ac.uk

Abstract

MOTIVATION:

Existing sequence assembly editors struggle with the volumes of data now readily available from the latest generation of DNA sequencing instruments.

RESULTS:

We describe the Gap5 software along with the data structures and algorithms used that allow it to be scalable. We demonstrate this with an assembly of 1.1 billion sequence fragments and compare the performance with several other programs. We analyse the memory, CPU, I/O usage and file sizes used by Gap5.

AVAILABILITY AND IMPLEMENTATION:

Gap5 is part of the Staden Package and is available under an Open Source licence from http://staden.sourceforge.net. It is implemented in C and Tcl/Tk. Currently it works on Unix systems only.

PMID:
20513662
PMCID:
PMC2894512
DOI:
10.1093/bioinformatics/btq268
[Indexed for MEDLINE]
Free PMC Article

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