Question: Are linked reads helpful for targeted re-sequencing applications?
Answer: Yes. For many applications, whole genome/whole exome re-sequencing is not required, instead targeted re-sequencing is the preferred method of investigation. Linked reads provide added value to Illumina paired-end reads in targeted re-sequencing applications as well as whole genome and whole exome experiments. This translates to better mapping and variant calling quality. To see our experimental data that shows these improvements please see our preprint here.