Single cell ‘omics and long-read technologies have developed rapidly in recent years enabling massively parallel sequencing of long cDNA and DNA fragments from single cells. These advances have been used for single cell isoform- and ATAC-seq sequencing and has revealed another layer of information unobtainable by short-read sequencing. However, long-read technologies are capable of sequencing much longer fragments than typical full-length cDNA or large ATAC-seq fragments and this capacity is underutilized in standard protocols.
We have developed Multi-Read Concatenated Library Sequencing (MiRCL-seq) to increase effective read output for Nanopore and PacBio sequencers. We describe this technique and its application in cost effective sequencing of full-length and targeted cDNA and ATAC-seq libraries from single cells obtained with the 10x Chromium platform. In addition, we show this technique allows sequencing of libraries that contain fragments not able to be sequenced by either short- or long-read sequencers alone. These results demonstrate the power of long-read sequencing and opportunities to develop new applications for sequencing short fragments on long read sequencers.