NISC - NIH Intramural Sequencing Center Platforms

Platforms

NextGen Sequencing Technologies

NISC currently employs the following NextGen sequencing technologies:

Illumina HiSeq 2500
Illumina MiSeq
PacBio RS II

Illumina HiSeq 2500 High Output

Sequence productivity and efficiency are ever increasing as software and chemistries are enhanced. Currently, this instrument produces up to 1 Tb of sequence per 6-day paired-end read run. Reads are 125 bases in length and are generated from each end of a DNA fragment in a paired-end read run, i.e., 2x125 b. Due to the extremely high quantity of sequence output, this technology is primarily useful for projects requiring a very large number of reads, such as whole genome, whole exome and multiplexed transcriptome experiments.

Illumina HiSeq 2500 Rapid

In addition to the ultra-high output mode, it can be operated in a flexible Rapid Run mode. A paired-end read run of 250 bases (2x250 b) will complete in 60 hours and generate up to 300 Gb of sequence. This capability is useful for large-scale sequencing of custom amplicon libraries and whole genome mate-pair libraries. A single read run of 50 bases (1x50 b) will complete in ~9 hours and produce 25-30 Gb of sequence. For samples requiring short reads, such as miRNA and DNA from ChIP isolation, these run conditions are appropriate.

Illumina MiSeq

MiSeq is a small scale benchtop sequencer using the same chemistry as the HiSeq models. This instrument is also compatible with the same Illumina libraries. MiSeq produces reads up to 300 bases in length from a paired-end read run (2x300 b) with a yield of ~10 Gb. This capability is primarily useful for sequencing microbial genomes and amplicons.

PacBio RS II

The PacBio RS II platform currently generates the industry's longest read length, while maintaining high consensus accuracy and unbiased coverage. The maximum read length is 40kb and the average read length is 14kb. This long read length allows the resolution of mobile elements and structural-variation events, and generates contiguous assemblies, allowing gaps to be filled and more genes to be annotated. This platform can rapidly and cost effectively generate finished microbial genome assemblies. Other applications include whole genome sequencing, full length 16s sequencing, epigenomes, isoforms, structural variants and CNVs. 1 SMRT cell generates up to 1 Gb of data and completes in 4 hours.