Gap5--editing the billion fragment sequence assembly.
BACKGROUND
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.


METHODS
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.
Bonfield
James K
JK
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK. jkb@sanger.ac.uk
Whitwham
Andrew
A
D001483:Base Sequence; D016208:Databases, Factual; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface