A SIROCCO pipeline has been developed for analysing the results of high throughput sequencing experiments. It is currently used most often for Illumina reads but can be used to process 454 reads as well.
So far, it has been successfully used for the processing of
• sRNA reads
• ChIP-Seq
• genomic DNA
Current analyses include:
• adaptor removal
• de-multiplexing of multiplex sequencing runs
• alignment against genomes, transcripts or other datasets
• generation of statistics/counts at each stage of the process
The group would like to offer this as a service to SIROCCO laboratories, particularly to those that do not yet have the infrastructure to perform the analysis themselves.
Interested groups that have (or plan to have) samples for analysis can contact bioinformatics@plantsci.cam.ac.uk.
The bioinformatics group is also happy to help with general bioinformatics problems.