Using shorter Illumina reads

Many people have asked if they can use their existing Illumina datasets with DISCOVAR – datasets that don’t meet the recommendations of ~60x coverage by 250 base paired reads from a ~700 bp PCR-free fragment library. We investigated and made some minor changes to the algorithm, embodied in release 46382 onwards, and it is now possible to use shorter reads from PCR libraries – with some caveats. We have successfully tested DISCOVAR on 100 base reads from a ~180 bp PCR fragment library, obtaining reasonable results but inferior to those generated from the recommended data. For more information on please see our FAQ.