BluePippin Optimized for Illumina’s Moleculo Kit

As Sage Science blog readers know, BluePippin is used throughout the genomics community for size-selecting larger fragments — we’ve gotten lots of attention for how well the tool performs with extremely long reads from the Pacific Biosciences sequencer, for example.

Now we can report that BluePippin has also been validated and optimized for use with the new Illumina TrueSeq Synthetic Long-Read DNA Library Prep Kit (TSSLR), based on the Moleculo technology.

The workflow was validated with a few different experiments. In one key project, we examined various size selection settings with the kit’s recommended DNA input (600 ng per lane) and shearing conditions. With the TSSLR team at Illumina, we agreed that a range mode of Bpstart=7,000 bp and Bpend=11,000 bp gives the best results.

In another project, we evaluated performance with different DNA input volumes. Starting with the recommended 600 ng of DNA and decreasing all the way to 100 ng, we found minimal changes in average fraction size. The TSSLR team determined that no adjustment to BluePippin settings is required for use with sample volumes as small as 100 ng.

This chart shows the results of using BluePippin with the TSSLR protocol for a low-concentration sample:


You can check out the official recommendations for using BluePippin sizing with the TSSLR kit in this prep guide from Illumina (starts on page 95).

Already working with the TSSLR kit? We’d love to hear about your experience and discuss how BluePippin sizing can improve your results. Ping us at

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