SolexaTools: An Open Source Sequence Analysis Framework

Brian O’ConnorNelson Lab

University of California, Los Angeles

http://solexatools.sourceforge.net

Illumina Data Flow

• We started with the basic data flow from the Illumina Genome Analyzer (images, sequence, quality score)

• Several components

needed to be written

– LIMS

– Alignment Plugins

– Reporting Tools

SolexaLIMS• Java: Spring &

Hibernate

• Used to gather

information

about each

sample needed

for proper

analysis

• Easy to use

SolexaPipeline

SolexaPipeline

Alignment Reports

BED & WIG files visualized in the UCSC Genome Browser

SolexaTools Release 1.0 release this month:

BLAT/ELAND/MAQ alignment algorithms

genomic/cDNA/digital gene expression/targeted sequencing/tagged sequences

LIMS supporting external/internal users

2.0 release: Support other sequencers (e.g. SOLiD)

Name change

Support other experimental methods

Better pipelining environment

Acknowledgements

• Jordan Mendler

• Zugen Chen

• Dmitriy Skvortsov

• Nils Homer

• Barry Merriman

• Stan Nelson

http://solexatools.sourceforge.net