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CAP TODAY Product Guides

Illumina, MiSeq

Illumina, MiSeq

Next-generation sequencing instruments, December 2017

Contact Information

5200 Illumina Way
San Diego, CA 92122

Name of instrument MiSeq
Name of model/Model has been upgraded —/no
Country where designed/Manufactured/FDA cleared or approved U.S./U.S./not required
First year sold in U.S./Outside U.S./First year installed 2011/2011/2011
Dimensions in inches (H × W × D)/Footprint of all instrumentation and computing hardware 20.6 × 27 × 22.2/~4.2 square feet
Equipment supplied with system/Automation for library preparation system is a single unit inclusive of amplification, paired-end sequencing, and analysis/yes
Necessary equipment not included with system and additional cost
Bioinformatics tools provided/For use by biologist or bioinformatician MiSeq Reporter/biologist; BaseSpace/biologist
Supplied with UPS/Entire workflow can occur in same lab no/yes
Clean room requirements/Electrical connection —/100–240 VAC at 50–60 Hz, 400 W
List price/Total list price for equipment needed to perform simplest and fastest workflow from amplification through variant calling (not typically found in lab) $99,000/—
Purchase options purchase, reagent rental, or lease (financing available)
Warranties offered first year included with instrument purchase, extended options available
Training included/Total time for standard install and basic training yes/<1 days
Training location/Follow-up training available on site/yes, extra charge
Instrument core performance:
Maximum No. of libraries amplified in single amplification event 384 for some applications
Read length/Percent bases >Q30 up to 2 × 300 bp/70 (for 2 × 300 bp)
Paired-end capability/Tag lengths/Spans yes/up to 2 × 300 bp/200–550 bp
Fragment/Tag lengths/Spans yes/up to 2 × 300 bp/200–550 bp
Mate-pair/Tag lengths/Spans yes/up to 2 × 150 bp/3–15 kb
Single-end/Tag lengths/Spans yes/1 × 600 bp/550 bp
RNA sequencing/Tag lengths/Spans yes/up to 2 × 300 bp/100–300 bp
ChIP sequencing/Tag lengths/Spans yes/up to 2 × 300 bp/100–300 bp
Bisulfite sequencing/Tag lengths/Spans yes/2 × 300 bp/100–300 bp
Output per run up to 15 Gb
Total time from library construction to variant calling to achieve output per run/Technical bench time/Bioinformatics time 4–55 hours depending on read length/2 hours/2 hours
Sample preparation:
Total time for generating standard gDNA library <2 hours
• Paired-end <2 hours
• Fragment <2 hours
• Mate-pair <2 days
• Single-end <2 hours
• RNA sequencing <9 hours
• ChIP sequencing <9 hours
• Bisulfite sequencing 5 hours
Hands-on time each:
• Paired-end 15 minutes
• Fragment <3 hours
• Mate-pair <2 hours
• Single-end 15 minutes
• RNA sequencing <5.5 hours
• ChIP sequencing <5.5 hours
• Bisulfite sequencing 3 hours
Equipment required for library construction standard lab equipment
Reagents and controls:
Cost per run $290–$1,530
Cost per sample*
Reagent tracking method on instrument RFID
Information contained in tracking method serial number, expiration date, lot and part numbers, number of cycles, PE-SR
Reagent shipping conditions/Storage conditions box 1: dry ice; box 2: gel pack/box 1: -15°–-20°C; box 2: 2°–8°C
Shelf life of amplification and sequencing reagents guaranteed 3 months
Controls introduced during creation of library/Sequencing control avail. yes/yes
Capable of complete walkaway automation for amplification, sequencing, and variant calling yes
Remote system monitoring yes
Instrument control software and devices to start run/for data analysis 10 minutes/2 hours
Total time required for setup of amplification, sequencing, and variant calling steps 10 minutes
Maximum No. of libraries sequenced in a single run up to 96 (384 for targeted RNA)
Types of maintenance plans available parts only, basic, comprehensive, advantage, dedicated on site
No. of field apps scientists and engineers based in U.S.
Weekly maintenance required/Monthly/Pre-run water wash/water wash/water wash
System offers secondary analysis software developed by instrument vendor yes
Variant report generated directly on instrument yes
Third-party analysis software available yes, BaseSpace apps store
Ability of software to detect mutations substitutions, indels, copy number changes
Total No. of peer-reviewed publications for this platform >5,300 publications
Published applications in pathology-related research
Fastest published turnaround time from sample to analyzed result 1.5 days (Koser, et al.)
Lowest published variant sensitivity level <5 percent (Harismendy, et al.)
Distinguishing features of sequencer (supplied by company) quality scores with >70% of bases higher than Q30 at 2 × 300 bp and >85% bases higher than Q30 at 2 × 75 bp and benchtop sequencer (per Loman, et al.) based on industry’s most-adopted sequencing technology (>5,300 publications); single instrument takes samples from library prep through secondary analysis with no ancillary equipment needed; simple, streamlined workflow with as little as 30 minutes hands-on time from sample to answer
*inclusive of sample prep, for multiple configurations, using 1 Mb and 30x average coverage per sample
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