Table 2.

Different applications of LRS technology.

LR-WGS
SMRT-WGS	De novo assembly and reference-based WGS with focus on structural variant calling (Chaisson et al., 2015a; Seo et al., 2016; Shi et al., 2016).
ONT-WGS	De novo assembly and reference-based WGS utilizing ultra-long reads to improve phasing and close gaps in the reference genome (Jain et al., 2018).
Targeted LRS
LR-PCR amplicon sequencing	Commonly used targeted approach with standard LR-PCR amplification of the target region followed by SMRT amplicon sequencing (Borras et al., 2017; Frans et al., 2018)
Hybridization-based capture	As for SR-NGS, hybridization-based target capture can be applied for LRS (Wang et al., 2015). Protocols are available for different vendors of bait-libraries.
No-Amp targeted SMRT sequencing	A standard PacBio SMRTbell library is created and a Cas9 guide RNA is designed adjacent to the region of interest. Digestion with Cas9 breaks open the SMRTbell molecules to enable ligation with a capture adapter. SMRTbell molecules that contain the capture adapter are enriched on magnetic beads and prepared for SMRT Sequencing (Tsai et al., 2017; Hoijer et al., 2018).
CATCH for ONT sequencing	CATCH (Cas9-assisted targeting of chromosome segments) is based on targeted fragmentation of DNA in vitro by Cas9, followed by separation of the target region from the rest of the genomic DNA by pulsed field gel electrophoresis and DNA isolation from the gel (Jiang et al., 2015; Gabrieli et al., 2018)
ONT Read until selective sequencing	Real-time data analysis that enables the selection of specific DNA molecules for sequencing by reversing the driving voltage across individual nanopores: this enables to proceed to sequence only molecules that are recognized to originate from a certain chromosome or region of interest (Loose et al., 2016).
LR-RNA-sequencing
SMRT-IsoSeq	The IsoSeq method of PacBio enables sequencing of full-length transcripts up to 15 Kb using SMRT sequencing, in turn eliminating computational transcript reconstruction and the need for a reference genome.
Direct ONT RNA-seq	By circumventing the bias prone elements in regular RNA sequencing, i.e., reverse transcription and PCR amplification of cDNA, Nanopore’s direct RNA-seq enables the direct detection of full-length RNA. This real-time single-molecule method is based on two adapters; (1) a poly(T)adaptor for recognition and binding of the polyadenylated messenger RNA, and (2) a pair of sequencing adaptors that ligate onto the overhang of the poly(T)adaptors and facilitate its capture by a nanopore (Garalde et al., 2018).
R2C2 method for ONT	Rolling Circle Amplification to Concatemeric Consensus (R2C2) method enables to generate a consensus from a single sequence read with many copies of an original molecule: this approach has been used to accurately produce full-length RNA transcript isoforms (Volden et al., 2018).