NGS Platforms


Comprehensive Sequencing Platforms for Epigenetic Services

Epigentek’s services utilize the most trusted and top-of-the-line sequencing equipment available for downstream analysis for use in our epigenetic services such as Methyl-Seq, ChIP-Seq, and RNA-Seq. A wide range of sequencing machines specialized for particular applications, including those manufactured by Illumina, Life Technologies, and PacBio, ensure the highest quality results for any of our customized services workflows. By selecting the optimal sequencing machine for your individual research design, we can promise reliable results, ensure minimal sequencing bias, and deliver to you highly accurate, publication-ready data.

All sequencing services are run on an Illumina HiSeq platform unless otherwise specified.

Illumina

MiSeq Illumina Sequencing ServicesIllumina MiSeq

This benchtop sequencer is ideal for small genome, amplicon, and targeted gene panel sequencing and is optimized for fast turnaround time and longer reads. Because it can read 50bps in only 6 hours, it can be used to ensure library protocols are optimal prior to sequencing on a larger-scale instrument like the HiSeq. The read length of 2 x 300 bp makes this sequencer ideal for small genomes or amplicon sequencing. Read more about the speed and simplicity of the trusted Illumina MiSeq sequencer.

Reads Passing Filter Per Flowcell Yields Per Flowcell Sequencing Time/Yield Per Flowcell No. of Lanes
Kit v2
• SR: 12 – 15M
• PE: 20 – 30M
Kit v3
• SR: 22 – 25M
• PE: 40 – 50M
Kit v2
• 750 Mb – 8.5 Gb
Kit v3
• 3.3 – 15 Gb
25PE: 6 hrs / 750 – 850 Mb
50SR: 6 hrs / 750 – 850 Mb
150PE: 24 hrs / 4.5 – 5.1 Gb
250PE: 39 hrs / 7.5 – 8.5 Gb
300PE: 55 hrs / 13.2 – 15 Gb
1 lane

SR: Single reads, PE: Pair-end reads, Mb: Megabases, Gb: Gigabases, M: Millions


 

NextSeq 500 Illumina Sequencing ServicesIllumina NextSeq 500

Mid Output or High Output. The NextSeq is ideal for sequencing of whole genomes, exomes, and transcriptomes and is flexible enough for low throughput sequencing, if desired. It takes advantage of new advancements in sequencing chemistry, SBS v2 sequencing reagents, in order to improve signal intensities and reduce false positives, false negative, and error rates. Two different types of flow cells are available depending on sample volume and coverage needs, configured for either mid output or high output. The NextSeq 500 enables one large whole genome sequencing experiment in a single run and utilizes new implementation of Real-Time Analysis (RTA) software that maximizes processing speed. Read more about the Illumina NextSeq 500 sequencer for analyzing whole genomes, exomes, and transcriptomes.

Reads Per Flowcell Sequencing Time/Yield per Flowcell No. of Lanes
Mid Output
High Output
Mid Output
High Output
Mid Output
High Output
SR: Up to 130M
PE: Up to 260M
SR: Up to 400M
PE: Up to 800M
75PE: 15 hr / 16.25 – 19.5 Gb
150PE: 26 hr / 32.5 – 39 Gb
75SR: 11 hr / 25 – 30 Gb
75PE: 18 hr / 50 – 60 Gb
150PE: ~29 hr / 100 – 120 Gb
4 lanes
(one single reservoir)

SR: Single reads, PE: Pair-end reads, Mb: Megabases, Gb: Gigabases, M: Millions


 

HiSeq 2000 Illumina Sequencing ServiceIllumina HiSeq 2000

High Output Run Mode. This sequencer uses two flowcells for every run. There is a total of 16 independent lanes (8 per flowcell). The 8th lane is assigned as a control for comparison, giving more accurate reads with reduced bias. Read lengths of 50 bp or 100 bp can be selected for your individual research project. Read more about the Illumina HiSeq 2000 sequencer.

Reads Per Lane Sequencing Time/Yield Per Flowcell No. of Lanes
SR: 150-200M
PE: 300-400M
50SR: 3 days / 7.5 – 10 Gb
100SR: 6 days / 15 – 20 Gb
50PE: 6 days / 15 – 20 Gb
100PE: 11 days / 30 – 40 Gb
8 lanes
(7 plus 1 control lane)

SR: Single reads, PE: Pair-end reads, Mb: Megabases, Gb: Gigabases, M: Millions


 

HiSeq 2500 Illumina Sequencing ServiceIllumina HiSeq 2500

Rapid Run Mode or High Output Run Mode. This powerful and efficient sequencer, which is optimal for large-scale genomics, is outfitted to operate by two modes. A rapid run mode enables long reads and a much faster run. The high output run mode produces similar results as the HiSeq 2000. Optimizations within the software improve the handling of libraries with low-diversity to ensure accurate results without a control lane for matrix and phasing estimates. The HiSeq 2500 rapid run mode offers a longer read length of 2 x 250 bp with 300 million reads per flow cell. Read more about the Illumina HiSeq 2500 sequencer suited for large-scale genomics.

Reads Per Flowcell Sequencing Time/Yield per Lane No. of Lanes
Rapid Run Mode
Rapid Run Mode
Rapid Run Mode
SR: 250-300M
PE: 500-600M
50SR: 8 hr / 12.5 – 15 Gb
100SR: 16 hr / 25 – 30 Gb
50PE: 16 hr / 25 – 30 Gb
100PE: 27 hr / 50 – 60 Gb
150PE: 40hr / 75 – 90 Gb
2 lanes
(physically connected)

SR: Single reads, PE: Pair-end reads, Mb: Megabases, Gb: Gigabases, M: Millions

Ion Torrent & PacBio

Ion Torrent PGM Sequencing ServiceIon Torrent PGM

The Personal Genome Machine (PGM) from Ion Torrent is a benchtop machine that uses semiconductor chip technology to provide massively parallel sequencing that is more affordable than typical optical systems. Producing one chip per run, the Ion Torrent PGM does not rely on optical signals, but on reliable, well-characterized natural biochemistry. The PGM™ System’s ion sensor detects a charge released by the hydrogen atom byproduct when a polymerase acts to incorporate a nucleotide into a DNA strand. Direct detection by this system enables the delivery of reliable and fast results and offers scalability and flexibility to suit your desired research needs and application. Read more about the Ion Torrent PGM’s technology.

Reads Passing Filter Per ChIP Yield per Chip (200bp/400bp kits) Sequencing Time Read Lengths
Ion 314 v2
• 400,000 – 550,000
Ion 316 v2
• 2 – 3M
Ion 318 v3
• 4 – 5.5M
Ion 314 v2
• 30 – 100 Mb
Ion 316 v2
• 300 Mb – 1 Gb
Ion 318 v2
• 600 Mb – 2 Gb
2.3 – 4.4 hrs 200bp and 400bp

SR: Single reads, PE: Pair-end reads, Mb: Megabases, Gb: Gigabases, M: Millions


 

Ion Torrent ProtonIon Torrent Proton

This benchtop sequencer utilizes the same technology as the Ion Torrent PGM, harnessing the power of natural biochemistry and semiconductor chip technology, but is intended for much larger-scale applications. Its high-throughput platform is capable of sequencing human-scale genomes, exomes, and whole transcriptomes with a read length of up to 200 bp. It can precisely detect variants, offers uniform coverage, and is sensitive enough to detect low frequency variants. The Ion Proton platform offers rapid, high-throughput sequencing with no complex optics and suits research projects investigating a range of high throughput genomic applications. We offer various high-throughput options that are available to suit your specific research needs. Read more about the multiplexing ability of the Ion Torrent Proton.

Reads Passing Filter Per ChIP Yield per Chip Sequencing Time Avg. Read Lengths
60 – 80 million 8 – 10 Gb 2.3 – 4.4 hrs 200bp and 400bp

SR: Single reads, PE: Pair-end reads, Mb: Megabases, Gb: Gigabases, M: Millions


 

PacBio RSII Sequencing ServicesPacBio RSII

This precise, high-performance optical sequencing machine is optimal for single molecule and real-time DNA sequencing and has expanded capabilities for epigenetic research. It relies on SMRT technology to provide extraordinarily long reads with impeccable accuracy, detecting variants with greater than 99.999% accuracy. It’s useful especially for epigenetics due to its ability to detect a wide range of DNA base modifications such as N6-methyladenine (m6A), N4-methylcytosine (m4C), DNA oxidative damage and other modified DNA bases. Read more about the PacBio RSII capabilities.

Reads Passing Filter Per Flowcell Yield Per SMRT Cell Sequencing Time Avg. Read Lengths
>50,000 P6-C4 chemistry
>500Mb
4 hrs 170bp

SR: Single reads, PE: Pair-end reads, Mb: Megabases, Gb: Gigabases, M: Millions