Illuminator
and
Illuminator data extractor
Illuminator is a new sequence alignment program for the output from Illumina GA-II clonal sequencers. It is aimed primarily at kilobase-sized reference regions, as would typically be used in the context of mutation detection.
Illuminator can map 5 million index-tagged 36-nt reads in under 2 minutes on a standard desktop computer. It uses an algorithm that indexes the reference sequence as a series of 8-mers and then matches the genomic reads to the 8-mer index, in a mutation-tolerant way permitting identification of single-nucleotide substitutions and indels.
Illuminator data extractor is a helper program that can convert various Illumina output file formats to those that can be easily used by Illuminator.
Illuminator Reference Files is another helper program that can quickly create Illuminator reference files for gene transcripts identified by the CCDS project.
Feature guides
Illuminator
A "walk-through" explanation, with screenshots, of how to use Illuminator:
Illuminator data extractor
A guide to the use of Illuminator data extractor:
Illuminator Reference Files
A guide to the use of Illuminator Reference Files:
Download
Illuminator is still under development. The download page currently offers a preview version of the Illuminator, Illuminator data extractor and Illuminator Reference Files programs, and also some sample data files, used in the examples shown in the online guides.
Illuminator, Illuminator data extractor and Illuminator Reference Files have been written by Ian Carr. Any feedback on these programs’ features or performance would be very welcome.
Citation
Carr IM, Morgan JE, Diggle CP, Sheridan EG, Markham AF, Logan CV, Inglehearn CF, Taylor GR, Bonthron DT.
Illuminator, a desktop program for mutation detection using short-read clonal sequencing.
Genomics 2011 Oct;98(4):302-9.