We have now successfully generated long read data for two species using Illumina's new Synthetic Long Read kit. This kit size selects 8-10kb fragments, spreads them in low concentrations across 384 (barcoded) wells, and completes a Nextera-like tagmentation of molecules in each well. Short reads are generated with a HiSeq, and long reads are synthesized in BaseSpace.

One lane of sequencing per sample generated ~500Mb of long read data, with an N50 for longer reads (those ≥1500bp) of ~6500. Now on to exploring the best practices for using these data to increase our scaffold lengths during genome assembly...