Platforms

NextGen Sequencing Technologies

NISC currently employs the following NextGen sequencing technologies:

Illumina NovaSeq X Plus
Illumina MiSeq i100
Illumina MiSeq
Ultima Genomics UG 100
Pacific Biosciences Revio
Oxford Nanopore Technology PromethION

Illumina NovaSeq X Plus

The NovaSeq X Plus is the latest high-output sequencer from Illumina. The standard run type on this instrument is paired-end 2x150b reads, with additional flexibility to generate shorter read lengths as needed. Due to the high volume of sequence data output (1.5 to 25 billion read-pairs per run), this technology is primarily useful for projects requiring a very large number of reads, such as genome, single-cell, or bulk RNA sequencing.

Illumina MiSeq i100

The latest low-output instrument from Illumina, the MiSeq i100 generates 5 to 100 million read-pairs per run. Read lengths vary from 2x50b to 2x500b making it a highly flexible instrument for short amplicon-based sequencing projects.

Illumina MiSeq

MiSeq is a small-scale Illumina benchtop sequencer primarily used for library QC prior to data runs on the NovaSeq X Plus.

Ultima Genomics UG 100

The UG 100 is a cost-effective high-output short read sequencer. Single-end reads of ~100-400b can be used for a variety of data intensive sample types, like single-cell and genome sequencing. Illumina libraries can be converted to run on this instrument, or UG specific libraries can also be sequenced. Unique to this platform is ppmSeq, a method that generates reads with very low error rates, on the order of 1 in a million, and is therefore suitable for accurate detection of low frequency single-nucleotide substitutions.

Pacific Biosciences Revio

The PacBio Revio platform generates long read lengths while maintaining high consensus accuracy. Multi-pass sequencing of both strands of the template is used to generate circular consensus (CCS) reads up to ~15-20 kb that can achieve accuracy > 99.9% (termed High Fidelity/HiFi reads) and also detect base modifications. This platform can generate sequence reads that support (1) high-quality genome assemblies; (2) detection of variants and haplotype phasing; (3) characterization of full-length isoforms; (4) epigenomics and (5) long-amplicon sequencing. For most applications, one SMRT cell/run generates 90-120 Gb of data and completes in ~30 hours.

Oxford Nanopore Technology PromethION

The ONT platform can generate short to ultra-long reads (>100 kb) from DNA templates as well as sequencing data directly from RNA templates. Both DNA and RNA modifications can be detected with this platform. Typical projects that are run on this platform take advantage of the unique aspects of the technology, ie very long reads for genome assembly or structural variant detection, detection of base modifications, or the ability to directly sequence RNA. The amount of data generated per flowcell is dependent on the sample type, with ultra-long genome libraries typically yielding ~20 Gb of reads >100kb (~40 Gb total) while direct RNA libraries yield a few million reads averaging ~1 kb.