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Thermo Fisher Scientific, 5500 Series Genetic Analyzers

Thermo Fisher Scientific, 5500 Series Genetic Analyzers

Next-generation sequencing instruments, December 2017

Contact Information

Thermo Fisher Scientific
5791 Van Allen Way
Carlsbad, CA 92008

Name of instrument 5500 Series Genetic Analyzers
Name of model/Model has been upgraded 5500, 5500xl, 5500xl Wildfire/—
Country where designed/Manufactured/FDA cleared or approved U.S., Japan/Japan/no
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 45.1 × 47.5 × 29.5/100 square feet
Equipment supplied with system/Automation for library preparation 5500xl workstation, instruction control software, installation kit, training/yes
Necessary equipment not included with system and additional cost Covaris S220 System: $44,500; UPS: $6,500; AB Library Builder system: $35,000; LifeScope workstation or cluster (or cloud) $22,500 or $48,000, respectively; Thermocycler: $5,000; SOLiD EZ Bead system (enricher, amplifier, emulsifier): $60,000 (replaced by on-FlowChip template preparation on 5500xl Wildfire)
Bioinformatics tools provided/For use by biologist or bioinformatician BAM file generation, SAM file generation, LifeScope Genomics Analysis Solution/ biologist
Supplied with UPS/Entire workflow can occur in same lab yes, for extra charge/yes
Clean room requirements/Electrical connection none/200–400 VAC
List price/Total list price for equipment needed to perform simplest and fastest workflow from amplification through variant calling (not typically found in lab) $595,000 (xl), $349,000 (5500), $250,000 (upgrade from SOLiD4)/$350,000
Purchase options
Warranties offered 1 year warranty
Training included/Total time for standard install and basic training yes/5 days
Training location/Follow-up training available on and off site/yes, for extra charge
Instrument core performance:
Maximum No. of libraries amplified in single amplification event 1,152
Read length/Percent bases >Q30 75 bp forward, 35 bp reverse/>85
Paired-end capability/Tag lengths/Spans yes/75 bp × 35 bp/150–300 bp
Fragment/Tag lengths/Spans yes/75 bp/150–300 bp
Mate-pair/Tag lengths/Spans yes/60 bp × 60 bp/0.5–10 kb supported; >10 kb enabled
Single-end/Tag lengths/Spans 75 bp/<3 kb/—
RNA sequencing/Tag lengths/Spans yes/75 bp × 35 bp/150–200 bp
ChIP sequencing/Tag lengths/Spans yes/35–75 bp/150–300 bp
Bisulfite sequencing/Tag lengths/Spans yes/75 bp/150–300 bp/—
Output per run 240 Gb
Total time from library construction to variant calling to achieve output per run/Technical bench time/Bioinformatics time 5–26 days (template prep: 2 hours on FlowChip, sequencing 2–21 days; data analysis: 2 days)/1–2 days/0.5–2 days
Sample preparation:
Total time for generating standard gDNA library
• Paired-end 3 hours
• Fragment 3 hours
• Mate-pair 2–3 days
• Single-end 3 hours
• RNA sequencing 2 days or 3 hours post-RNA extraction
• ChIP sequencing 3 hours post ChiP
• Bisulfite sequencing 3 hours
Hands-on time each:
• Paired-end 30 minutes
• Fragment 30 minutes
• Mate-pair 8 hours
• Single-end 30 minutes
• RNA sequencing 2 hours
• ChIP sequencing 30 minutes post ChiP
• Bisulfite sequencing 45 minutes
Equipment required for library construction standard lab equip., magnetic bead separator, Covaris system, AB library building
Reagents and controls:
Cost per run $2,000 5500xl Wildfire
Cost per sample* 1Mb, 200x to 2,000x coverage per sample, in one-lane run of multiplexed samples (includes library prep): $116 (12 samples), $108 (24 samples), $104 (48 samples), $102 (96 samples)
Reagent tracking method on instrument real-time reagent monitoring
Information contained in tracking method current reagent volume predicted time to replenish reagents
Reagent shipping conditions/Storage conditions -20°C, 4°C, and ambient/-20°C, 4°C, and ambient
Shelf life of amplification and sequencing reagents 1 year
Controls introduced during creation of library/Sequencing control avail. yes/no
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 ICS on system workstation/LifeScope or cloud
Total time required for setup of amplification, sequencing, and variant calling steps 5–26 days
Maximum No. of libraries sequenced in a single run 1,152
Types of maintenance plans available AB Assurance (fixed-price planned maintenance)
No. of field apps scientists and engineers based in U.S. 24 field applications scientists, 31 engineers
Weekly maintenance required/Monthly/Pre-run
System offers secondary analysis software developed by instrument vendor yes
Variant report generated directly on instrument no
Third-party analysis software available yes, Partek, SoftGenetics, GenoLogics, CLC Bio
Ability of software to detect mutations substitutions, indels, copy number changes
Total No. of peer-reviewed publications for this platform 225
Published applications in pathology-related research 60 related publications
Fastest published turnaround time from sample to analyzed result 3 months
Lowest published variant sensitivity level <1 percent
Distinguishing features of sequencer (supplied by company) two-base encoding and exact call chemistry delivers 99.99% accuracy, which enables detection of low-frequency variants; pay-per-lane sequencing; application-per-lane sequencing
*inclusive of sample prep, for multiple configurations, using 1 Mb and 30x average coverage per sample
Note: a dash in lieu of an answer means company did not answer question or question is not applicable
All information is supplied by the companies listed. The tabulation does not represent an endorsement by the CAP.