NGS Sequencing Support—Getting Started

The Ion SingleSeq 96 Kit includes reagents to extract, amplify, and barcode genomic DNA for preparation of libraries from up to 96 samples. For a detailed list, please go here.

Ion S5 2X Cleaning Solution is used to perform a pulse clean of your Ion S5 Sequencer (GeneStudio S5/GeneStudio S5 Plus/GeneStudio S5 Prime systems and Ion S5/Ion S5 XL systems) to either recover the instrument performance from a diagnosed solid-state buffer leak or perform preventative maintenance if the instrument has not been used for several months.

Ion S5 2X Cleaning Solution is compatible with GeneStudio S5/GeneStudio S5 Plus/GeneStudio S5 Prime systems and Ion S5/Ion S5 XL systems.

Go to "System tools" and select "pulse clean". The instrument must already have been cleaned after a run.

It takes approximately 47 mins to do a "pulse clean".

Please see the Ion PGM™ System Product Selection Guide for a list of available products for the Ion PGM™ System workflow organized by application.  

Each Ion PGM™ sequencing kit includes reagents and materials for four initializations. The number of runs per initialization will depend on the desired read length.

The Ion PGM™ Sequencing 200 Kit v2 (Cat. No. 4482006) supports two runs per initialization (or eight runs per kit) for 200-base read sequencing. For ≤100-base read sequencing, there are enough reagents to support three runs per initialization (or twelve runs per kit).

The Ion PGM™ Sequencing 400 Kit (Cat. No. 4482002) supports one run per initialization (or four runs per kit) for 300- and 400-base read sequencing.

Firmware updates for Ion instruments are included with the latest version of Torrent Suite Software. First, download and install the latest version of Torrent Suite Software on your Torrent Server. Once completed, your Ion PGM™ System should alert you that an update is available. You can also start the update process from the Options menu. From the Main menu, select Options, then Updates, Released Updates, and Check. Once your Ion PGM™ system has detected the update, press the Update button to begin the process. Instructions to update the Ion PGM™ Sequencer can also be found in the Appendix of the Ion PGM™ sequencing kit user guides.

The number of samples that can be multiplexed in a single sequencing run depends on the capacity of the chip, the size of the library, and the required coverage. A table of approximate capacities based on the size of the library and chip can be found in the Ion AmpliSeq Preparation User Guide within the section “Strategies for combining Ion AmpliSeq libraries.”

When performing two sequencing runs from the same initialization, the second run must be started within 27 hours after initialization.

No, the Ion PI Hi-Q sequencing chemistry is only compatible with the Ion PI Chip v3. Using the Ion PI Chip v2 will result in lower loading and data throughput. 

Yes, an Ion PI v2 chip can be used for the initialization. Ensure that the PI Hi-Q initialization program is selected, and an Ion PI Chip v3 is used for the sequencing run.

No. The Ion PI™ Chips v2 are not optimized for use with the Ion PI™ Hi-Q™ Chef Kit chemistry. We recommend using the Ion PI™ Chips v3, which have been pretreated during manufacturing and optimized for use with the Ion PI™ Hi-Q™ Chef Kit chemistry.

The Ion PI™ Chips v3 have a shelf life of 9 months from manufacturing. However, please be aware that when you order the chips, time may have passed since manufacturing. To request the chips with the longest expiration date available, please contact Customer Care by phone to see which lots are in stock.

The initialization is stable for 24 hours after initialization. However, we still recommend that you begin the second sequencing run right after the first run is completed.

Yes, up to 3 barcoded exome libraries can be run on an Ion P1™ Chip depending on the coverage and depth desired. As the number of libraries on a single chip increases, the average coverage depth decreases.

The recommendation is 2 exomes per chip.  We can confidently call germ line mutations at 20 X coverage. You need ~ 30 M mapped reads per library, so since the minimum number of reads per chip is 60 million reads, that is 2 exomes per chip.

The Ion PI Chip Kit v3 yields 60-80 million reads.

No, the chip in the Ion PI Chip Kit v3 comes pre-treated, which reduces hands-on time for chip preparation.

Initialization takes 35 minutes for both the Ion S5™ and Ion™ S5™ XL Systems.

No, the Ion S5™ and Ion™ S5™ XL Systems have an onboard air compressor and tank to store pressurized air.

No, the instrument will give a warning message regarding the expired reagents, but will not prevent you from running the instrument.

We expect that applications currently supported on the Ion PGM™ and Ion Proton™ Systems will be supported on the Ion S5™ and Ion™ S5™ XL Systems. However, not all applications have been tested or demonstrated yet.

For 200 bp sequencing, it will yield 0.6 - 1.0 Gb. For 400 bp sequencing, it will yield 1.2-2 Gb.

For 200 bp sequencing, it will yield 3-4 Gb. For 400 bp sequencing, it will yield 6-8 Gb.

For 200 bp sequencing, it will yield 10-15 Gb. 400 bp sequencing is not supported on the Ion 540™ Chip.

No, the W2 solution in the Ion S5™ and Ion™ S5™ XL Systems is supplied at the correct pH, so the auto pH step is not necessary.

Unlike the Ion PGM™ and Ion Proton™ Systems, the sequencing reagents for the Ion S5™ and Ion™ S5™ XL Systems come with a cleaning solution bottle, which the instrument uses to automatically clean itself after each run.

You can perform either one or two runs per initialization on the Ion S5 and Ion S5 XL systems, depending on the read length of each run.  Two runs per initialization are compatible with 200 bp reads whereas only one run per initialization is compatible with 400 bp reads.

• For two 200 bp runs per initialization on the Ion S5/S5XL and Ion Chef systems, using the Ion 520 or Ion 530 chip, we recommend using the Ion 520 & Ion 530 Kit-Chef (2 sequencing runs per initialization), Cat. No. A30010.
• For two 200 bp runs per initialization on the Ion S5/S5XL and Ion Chef Systems, using the Ion 540 chip, we recommend using the Ion 540 Kit-Chef (2 sequencing runs per initialization), Cat. No.A30011.
• For one 200 bp or one 400 bp run per initialization on the Ion S5/S5XL and Ion Chef systems, using the Ion 520 or Ion 530 chip, we recommend using the Ion 520 & Ion 530 Kit-Chef, Cat. No. A27757.
• For one 200 bp or one 400 bp run per initialization on the Ion S5/S5XL and Ion Chef systems, using the Ion 540 chip, we recommend using the Ion 540 Kit-Chef, Cat. No. A27759.
• For one 400 bp run or two 200 bp runs per initialization on the Ion S5/S5XL and Ion OneTouch2 systems, using the Ion 520 or Ion 530 chip, we recommend using the Ion 520 & Ion 530 Kit-OT2, Cat. No. A27751.
• For one or two 200 bp runs per initialization on the Ion S5/S5XL and Ion OneTouch2 systems, using the Ion 540 chip, we recommend using the Ion 540 Kit-OT2, Cat. No. A27753.

Note: 400 bp runs are not compatible with the Ion 540 chip.

The initialization is stable for 24 hours. Both runs, if performing two 200 bp runs, must be started within 24 hours of the end of the initialization.

Using the Ion 520 & 530 Kit - Chef with the Ion 520 Chip will yield up to 5 M reads. Using the Ion 520 & 530 Kit - Chef with the Ion 530 Chip will yield up to 20 M reads.

The Ion 520 & 530 Kit - Chef (Cat. No. A27757) contains reagents and consumables for performing 8 runs, either 200 bp or 400 bp (1 run per initialization). The Ion 520 & 530 Kit - Chef (Cat. No. A30010) contains reagents and consumables for performing eight 200 bp runs (2 runs per initialization).

No, the Ion 520 & 530 Kit - Chef (Cat. No. A30010), which can perform 2 runs per initialization, can only perform 200 bp sequencing. Use the Ion 520 & 530 Kit - Chef (Cat. A27757) if you would like to perform 400 bp sequencing runs. Please note that you can only perform 1 run per initialization with this kit.

The Ion 520 & 530 Kit - Chef is compatible with Torrent Suite Software v5.0 and above.

No, you should not run the post-run clean after the first Ion S5/Ion S5 XL run. Make sure that you DESELECT the post-run clean option in the run setup for the first run. Failing to do so will lead to the instrument automatically performing the cleaning procedure, which will waste the reagents for the second run. RESELECT the post-run clean for the second run so that the instrument can perform the cleaning procedure.

The Ion S5/Ion S5 XL wash and cleaning bottles can be placed in regular plastic recycling bins. The sequencing reagent cartridge must be disposed of in the hazardous waste bin.

The Ion 540 Kit - Chef (Cat. No. A27759) contains reagents and consumables for performing eight 200 bp runs (1 run per initialization). The Ion 540 Kit - Chef (Cat. No. A30011) contains reagents and consumables for eight 200 bp runs (2 runs per initialization).

The initialization is stable for 24 hours. Both runs, if performing two 20 0bp runs, must be started within 24 hours of the end of the initialization.

The Ion 540 Kit - Chef (Cat. No. A27759) contains reagents and consumables for performing eight 200 bp runs (1 run per initialization). The Ion 540 Kit - Chef (Cat. No. A30011) contains reagents and consumables for performing eight 200 bp runs (2 runs per initialization).

No, the Ion 540 Kit - Chef can only perform 200 bp sequencing runs.

The Ion 540 Kit - Chef can yield up to 80 M reads.

The Ion 540 Kit - Chef is compatible with Torrent Suite Software v5.0 and above.

The package includes the Ion GeneStudio S5 Prime System and SmartStart orientation. SmartStart orientation is carried out by a Field Application Scientist (FAS) to get you up and running quickly in your lab and reduce downtime. It includes:
- 1 day technology overview and instrument workflow training
- 1 day hands-on application workflow training
- 10 hours bioinformatics consultancy

The package includes the Ion GeneStudio S5 System and SmartStart orientation. SmartStart orientation is carried out by a Field Application Scientist (FAS) to get you up and running quickly in your lab and reduce downtime. It includes:
- 1 day technology overview and instrument workflow training
- 1 day hands-on application workflow training
- 10 hours bioinformatics consultancy

The package includes the Ion GeneStudio S5 Plus System and SmartStart orientation. SmartStart orientation is carried out by a Field Application Scientist (FAS) to get you up and running quickly in your lab and reduce downtime. It includes:
- 1 day technology overview and instrument workflow training
- 1 day hands-on application workflow training
- 10 hours bioinformatics consultancy

Ion 510 Chip, Ion 520 Chip, Ion 530 Chip, and Ion 540 Chip are compatible with the Ion GeneStudio S5 System.

The Ion GeneStudio S5 System has a maximum throughput/day of 15 Gb.

No, the Ion GeneStudio S5 System's analysis server is contained within the sequencer itself.

No, the analysis of the first chip must complete before the sequencing run of the second chip begins.

No, the server is contained inside the sequencer itself.

The Ion GeneStudio S5 Plus System takes 11.5 hours to run an Ion 550 Chip.

The Ion GeneStudio S5 Plus System has a maximum throughput/day of 30 Gb (2 Ion 540 Chips).

Yes, the Ion GeneStudio S5 Prime System has a separate server.

Ion 510 Chip, Ion 520 Chip, Ion 530 Chip, Ion 540 Chip, and Ion 550 Chip are compatible with the Ion GeneStudio S5 Prime System.

The Ion S5 GeneStudio Prime System takes 8.5 hours to run an Ion 550 Chip.

The Ion S5 GeneStudio Prime System has a maximum throughput/day of 50 Gb (2 Ion 550 Chips).

The Genexus Sequencing Kit provides the materials required to perform two initializations and automated sequencing of two multilane chips using the Genexus Integrated Sequencer.

Yes, the Genexus Sequencing Kit reagents and supplies can be used with both 200-400 base-read Ion AmpliSeq library chemistry and Ion AmpliSeq HD library chemistry runs.

The coupler allows the pipettor to dispense reagents into the desired chip lane and it shuttles the chip between the loading and sequencing area on the Genexus platform. Every time you change the chip, you should change the coupler.

The GX5 chip generates 12-15 million sequencing reads per lane, or 48-60 million reads per chip. The four-lane chip design provides maximum flexibility for sample processing, enabling sequencing of one to four lanes per run, with the in-use stability to utilize any remaining lanes within two weeks of the initial run.

If the number of sample reads is very low, and CF-1 metrics fail QC, there could be a potential issue with the chip/coupler.

Genexus Library Strips 1 and 2-AS for standard Ion AmpliSeq library-based chemistry provides eight pairs of strips/kit, to perform automated library preparation using the Genexus Integrated Sequencer.

Each library strip pair is needed to create an Ion AmpliSeq library and supports up to 4 barcodes.
So 8 strip pairs x 4 = up to 32 DNA or RNA samples/run

Genexus Library Strips 1 and 2-HD (Cat. No. A40255) for Ion AmpliSeq HD library-based chemistry provides eight pairs of strips/kit, to perform automated library preparation using the Genexus Integrated Sequencer.

Each library strip is needed to create an Ion Ampliseq HD library and supports up to 4 barcodes.
So 8 strip pairs x 4 = up to 32 DNA or RNA samples/run

When necessary, the software will alert the user during the run plan setup that not enough barcodes are available.

Genexus Templating Strips 3 and 4-GX5 (Cat. No. A40263) can be used with both Ion AmpliSeq library chemistry and Ion AmpliSeq HD library chemistry runs.