Question: Can I sequence Genome or Exome libraries with fewer cycles than the recommended 2x150 bp?
Answer: For Exome libraries, we have tested sequencing with a 2x100bp configuration and we did not observe a difference in mapping performance or SNP sensitivity. We have not tested this explicitly on Genome libraries, and thus it is difficult to speculate what the degree of performance degradation would be. We would expect some degradation of MAPQs, indel calling accuracy, and small SV calling sensitivity. Based on our experience with Exome libraries, SNP sensitivity should stay fairly constant.
Nevertheless, we strongly recommend 2x150bp for optimal results and application performance.
Products: Genome, Exome