Library Preparation > General > FAQ

• Can Illumina RNA Prep with Enrichment library prep and enrichment reagents be purchased separately?

• Can PhiX and denatured PhiX be stored and used again?

• Can RSB be used as a substitute for RSB + Tween 20 when sequencing on the NextSeq 1000/2000?

• Can library preparation reagents be stored in a frost free freezer?

• Can samples be sent to Illumina for sequencing; does Illumina offer sequencing as a service?

• Can wells in index plates be used more than once?

• Catalog/Reference numbers for IDT for Illumina DNA/RNA UD and Illumina DNA/RNA UD Indexes

• Denature and dilution FAQ for Illumina DNA PCR Free

• Does library loading differ between MiSeq Micro and Nano flow cells?

• How much PhiX to spike in for well balanced, base diverse libraries?

• How to perform library heat denaturation (heat shock) before sequencing?

• How to prepare < 2 nM libraries for sequencing on NovaSeq X/X Plus

• Hybridization Buffer (HT1) and Resuspension Buffer (RSB) alternatives and purchasing availability

• IDT for Illumina TruSeq Unique Dual (UD) Index kit FAQs for kit configurations and usage

• Indexed Sequencing workflows with 5' to 3' directionality

• Information about the TruSeq index adapter plate fixture

• Introducing the Illumina DNA/RNA UD Indexes

• Link to the Sequencing Methods Explorer

• Plate layout for the Illumina DNA/RNA UD Indexes (v3)

• Product page and support page links for Illumina DNA Prep with Enrichment (S) Tagmentation

• Product page and support page links for Illumina RNA Prep with Enrichment, (L) Tagmentation

• Product page and support page links for TruSeq DNA Exome

• Product page and support page links for TruSeq Methyl Capture EPIC

• Product page and support page links for TruSight Cancer bundled with TruSight Rapid Capture

• Product page and support page links for TruSight Myeloid

• Should index reads be performed if only one library is being sequenced?

• Should indexes be read when sequencing a single library?

• What are the Illumina sequencing primer sequences?

• What are the index sequences for the AmpliSeq CD Indexes Large Volume kit for Illumina?

• What do (S), (M), and (L) mean in Illumina library prep kit names?

• What is the concentration of Illumina adapters and primers?

• What is the difference between a single and dual indexed library?

• What is the minimum library size that can be sequenced?

• Where are the sequences and plate positions of Illumina indexes?

• Where to find the reference sequence used for phiX alignment?

• Which TruSeq index kits come in plate or tube format?

• Which computer operating systems are compatible with Illumina Experiment Manager (IEM)?

Library prep and enrichment reagents can be ordered bundled or as separate reagents*****. This supports processing samples at different plexities than recommended by Illumina.

Bundled library prep and enrichment reagents

• 20040536 Illumina RNA Prep with Enrichment, (L) Tagmentation (16 Samples)

  • Supports 1-plex enrichments (16 enrichments)

• 20040537 Illumina RNA Prep with Enrichment, (L) Tagmentation (96 Samples)

  • Support 3-plex enrichments (32 enrichments)

Individual library prep reagents (pre-enrichment)

• 20040542 Illumina RNA Prep, (L) Tagmentation (16 Samples)

Individual enrichment reagents

• 20040540 Illumina RNA Fast Hyb Enrichment (16 Samples)

Note: Indexes are not included and must be purchased separately*****.

• Recommended indexes:

  • 20091654 Illumina DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples)

  • 20091656 Illumina DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples)

  • 20091658 Illumina DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples)

  • 20091660 Illumina DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples)

• Additional indexes (Orders accepted until January 29, 2025 or until inventory is depleted):

  • 20027213 IDT for Illumina DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 Samples)

  • 20027214 IDT for Illumina DNA/RNA UD Indexes Set B, Tagmentation (96 Indexes, 96 Samples)

  • 20042666 IDT for Illumina DNA/RNA UD Indexes Set C, Tagmentation (96 Indexes, 96 Samples)

  • 20042667 IDT for Illumina DNA/RNA UD Indexes Set D, Tagmentation (96 Indexes, 96 Samples)

Note: The Illumina Exome Panel and Respiratory Virus Oligo Panel v2 (RVOP v2) enrichment oligo panels are not included and must be purchased separately.

*The Respiratory Pathogen ID/AMR (RPIP) Enrichment Panel is configured as a bundled kit. The kit contains library prep reagents to prepare 96 samples with 32 3-plex enrichments, indexes (Set A or Set B), enrichment oligo panel, and analysis with the IDbyDNA RPIP Explify app. The last order date for kits that ship with IDT for Illumina DNA/RNA UD Indexes will be January 30, 2025, with last ship date of March 30, 2025 per PCN2024-1649. After these dates, kits will ship with Illumina DNA/RNA UD Indexes instead.

Store non-denatured, undiluted 10 nM stock PhiX at -25°C to -15°C until the expiration date.

Store non-denatured, diluted 4 nM PhiX at -25°C to -15°C for up to 3 months.

Store the denatured, diluted 20 pM PhiX at -25°C to -15°C for up to 3 weeks. After 3 weeks, cluster numbers tend to decrease.

For use with the NextSeq 500/550: Store the denatured 1.8 pM PhiX at -25°C to -15°C for up to 2 weeks. After 2 weeks, cluster numbers tend to decrease.

Resuspension Buffer (RSB) cannot be used as a substitute for RSB + Tween 20 when sequencing with NextSeq 1000/2000 flow cells. If RSB + Tween 20 is not available, substitute 10 mM Tris-HCl, pH 8.5 with 0.1% Tween 20.

Frost-free freezers undergo cycles of light thawing to prevent the formation of frost build up. Therefore, frost-free freezers are not generally recommended due to variation in temperature. It can be helpful to use freezers that retain temperature-logging data to confirm that reagents are kept within the recommended range at all times.

Illumina does not provide sequencing as a service, generally. Illumina recommends using third-party sequencing service providers or core facilities for library preparation and/or sequencing services.

For recommendations for service providers, contact the Illumina sales team.

Illumina does not recommend re-using index wells in plates to avoid cross-well contamination.

For Illumina consumables, there are reference (ref) numbers at the kit, box, and tube/component levels. Orders are placed using the kit level catalog numbers. A single kit can contain multiple boxes, which in turn can contain multiple tubes or components. To simplify the purchasing experience, the Illumina website only displays the orderable kit reference or catalog numbers.

Below are the kit (blue), box (red), and component (black) reference numbers for the following Illumina index kits:

• IDT for Illumina DNA/RNA UD Indexes Sets A-D, Tagmentation

• IDT for Illumina RNA UD Indexes Sets A-D, Ligation

• Illumina DNA/RNA UD Indexes Sets A-D, Tagmentation

• Illumina RNA UD Indexes Sets A-D, Ligation

The "DNA/RNA…Tagmentation" kits include a single index plate each; whereas, the "RNA…Ligation" kits include the same respective index plate and also include an anchor plate. Note that the IDT for Illumina DNA/RNA UD Indexes Sets A-D (20027213, 20027214, 20042666, 20042667) have been announced to be obsolesced, and the last order date for these kits is January 30, 2025, as announced in Product Obsolescence Notice (PON) 2023-1440. Illumina recommends ordering the new Illumina DNA/RNA UD Indexes Sets A-D if possible (20091654, 20091656, 20091658, 20091660).

For more information on the differences between the Tagmentation and Ligation sets, and with which library prep kits they are associated, see the Understanding the differences between Illumina index chemistries and anchor function article.

Which Denature & Dilute protocol to follow for NovaSeq 6000 and for other supported instruments? If protocol A/standard protocol, is NaOH added twice? (Once mid-protocol (HP3 reagent) and then again as per Denature & Dilute guide protocol)

• Follow Protocol A for standard workflow for the NovaSeq 6000 with standard loading and other instruments, and yes, add the NaOH during denaturation step. It will prevent formation of any secondary structures.

• For the NovaSeq 6000 Xp workflow, follow Protocol B.

Do libraries need to be heat shocked/heat treated to make sure it is single stranded DNA like with Nextera XT, which also uses bead-based normalization? If so, where are the instructions? No. NaOH denaturation will take care of secondary structures. Additional heat denaturation is not required.

If denaturation prior to clustering was omitted—will the data be okay? What is the performance impact? This method of clustering is not supported. However, because Illumina DNA PCR-free generates single stranded DNA (ssDNA) libraries, the libraries may still cluster and generate high quality data, though this cannot be guaranteed. It is possible to see lower quality, lower data output (lower cluster density or percent occupancy), or run failure.

Libraries will be denatured and diluted to the same final volume of 600 µL regardless of MiSeq flow cell is used.

If a library loading concentration has been optimized using MiSeq v2 reagents with a standard flow cell, the same loading concentration should be used with a Micro or Nano flow cell. If a library loading concentration has been optimized with MiSeq v3 reagents, the loading concentration may need to be slightly lowered when using a Micro or Nano (or standard output v2) flow cell due to the lower cluster density supported with MiSeq v2 reagents.

The PhiX sequencing control is not required for runs where the library pool is well-balanced in terms of base diversity, such as whole-genome and RNA-seq libraries; however, Illumina recommends spiking at least 1% PhiX into the library pool as a sequencing control and in order to obtain the error rate metric.

For amplicon-based libraries, highly structured or GC-rich libraries, and select other library types, cluster density consistency improves when the library is heat denatured before loading the pool onto the instrument. This method is optional for other libraries types as well.

Use the following steps to perform a heat denaturation.

1. After NaOH denaturation of the sequencing library, dilution with HT1 to the final loading concentration, and optional phiX addition, incubate the diluted library pool at 96°C for 2 minutes using a heat block.

2. After the heat incubation, invert the tube 1-2 times to mix.

3. Quickly move the library to an ice water bath for 5 minutes. This quick cooling step helps lock the library in its single stranded form.

4. Proceed immediately to cluster generation.

The tables in the Denature and Dilute Protocol Generator for NovaSeq X Plus provide the µl of 2 nM libraries + µl of RSB to combine to obtain the specified Final Loading Concentration (pM) after the addition of NaOH and Pre-load Buffer. The following math accounts for the later additional dilutions with NaOH and Pre-Load Buffer. Note that sequencing of libraries less than 2 nM has not been validated by Illumina, and is not supported.

1. Measure the library pool concentration in pM (Y)

• eg, 1000 pM

1. Determine the final target loading concentration in pM (X)

• eg, 180 pM

1. Calculate the volume of library and RSB required using the following formula:

   1. (Y pM) (Z µl) = (5*X) (volume needed by flow cell type)

   2. Volume needed by flow cell type = 34 µl for 10B or 1.5B, and 56 µl for 25B flow cells

   3. Volume library needed = Z

   4. Volume RSB needed = (Volume needed by flow cell type) - Z

2. Move to step 4 "[Optional] Spike in 1-2% nondenatured PhiX as follows" of the "Dilute Libraries and Add PhiX Control" section of the protocol if adding PhiX, or the "Denature Libraries" section if not adding PhiX.

Example calculation for 1.5 B or 10B flow cell: (1000 pM) (Z µl) = (5 * 180 pM) (34 µl)

Volume library needed (Z) = 30.6 µl Volume RSB needed = 34 - 30.6 = 3.4 µl

Example calculation for 25B flow cell: (1000 pM) (Z µl) = (5 * 180 pM) (56 µl)

Volume library needed (Z) = 50.4 µl Volume RSB needed = 56 - 50.4 = 5.6 µl

**Hybridization Buffer (HT1) is used for the final library dilution(s) following denaturation, prior to sequencing, and Resuspension Buffer (RSB) is a commonly used buffer in Illumina library preparation kits.

What can be used as a substitute for RSB when diluting libraries prior to sequencing?**

• 10 mM Tris-HCl, pH 8.5 with 0.1% Tween 20.

• 10 mM Tris-HCl, pH 8.5.

• Nuclease free water can also be used*. (*Unless sequencing on NextSeq 1000/2000, in which case the RSB with Tween reagent is critical for clustering; if RSB with Tween is not available, use the first option above as a substitute for RSB with Tween.)

What can be used as a substitute for HT1? There are no officially recommended substitutes. Use HT1.

Is RSB sold individually? RSB is not available for purchase individually at this time.

How can RSB with Tween be ordered, and when should it be used? RSB with Tween must be used when diluting libraries for sequencing on the NextSeq 1000/2000. It is included in the NextSeq 1000/2000 sequencing reagent kits.

Is HT1 sold individually? Yes, it can be purchased here.

Is HT1 included in the Nextera XT library prep kits the same as the HT1 that is included in sequencing reagent kits? Yes, the composition of the HT1 is the same in both, but the part numbers are different.

The full support page for the IDT for Illumina TruSeq Unique Dual (UD) Index kits is available here.

What is the layout of the index plate? Index plate layout is on the page here.

What are the catalog numbers for the IDT for Illumina TruSeq UD Indexes, and which library preparation kits are compatible?

• IDT for Illumina - TruSeq DNA UD Indexes are compatible with TruSeq DNA PCR Free and TruSeq DNA Nano library prep kits.

  • IDT for Illumina - TruSeq DNA UD Indexes v2 (96 Indexes, 96 Samples) 20040870

• IDT for Illumina - TruSeq RNA UD Indexes are compatible with TruSeq Stranded mRNA, and TruSeq Stranded Total RNA library prep kits.

  • IDT for Illumina - TruSeq RNA UD Indexes v2 (96 Indexes, 96 Samples) 20040871

Which Illumina sequencing platforms are compatible with IDT for Illumina TruSeq UD v2 indexes? IDT for Illumina TruSeq UD indexes are compatible with all Illumina sequencing platforms.

Do any of index sets collide or match any of other Illumina index kits? The IDT for Illumina TruSeq UD v2 indexes are not designed to be used with any other Illumina index sets.

Are there considerations for low-plexity pooling? Yes, there are recommended index combinations for 2-plex though 96-plex within the plate. For more information, see the Index Adapter Pooling Guide.

What are the storage and shipping conditions of these index kits? The reagents are shipped on dry ice and must be stored at -25°C to -15°C upon arrival.

Are the IDT for Illumina TruSeq UD Indexes compatible with all products from Illumina? No; consult the library preparation kit product page for index kit compatibility.

Do the indexes need to be diluted prior to use? No, do not dilute the indexes before use; the indexes are supplied at the working concentration.

Does the index volume used per sample need to be adjusted when using the IDT for Illumina TruSeq UD v2 Indexes? No, there is no change to the index volume required for compatible library preparation workflows (2.5 µl used per sample).

Will using the IDT for Illumina TruSeq UD v2 indexes change the final library QC traces? Libraries prepared with the IDT for Illumina TruSeq UD Indexes are expected to migrate similarly to the libraries prepared with Combinatorial Dual (CD) or single index adapters.

Single-Indexed SequencingThe single-indexed sequencing workflow applies to all Illumina sequencing platforms, where an Index Read follows Read 1.

Dual-Indexed Workflow on a Paired-End Flow Cell

Forward Strand Workflow: MiniSeq with Rapid Reagent kits and the MiSeq.

Note: While MiniSeq Rapid reagents allow for dual indexing, Read 2 cannot be performed with the MiniSeq Rapid reagent kit.

Reverse Complement Workflow: iSeq 100, MiniSeq with Standard reagent kits, NextSeq 500/550, NextSeq 1000/2000, NovaSeq 6000 with v1.5 reagent kits, and NovaSeq X Series.

For more information, see the Indexed Sequencing on Illumina Systems Guide.

What is the TruSeq index adapter plate fixture?

This plate fixture holds the narrow Nextera XT index primer tubes and TruSight Myeloid index adapter tubes along with the 96-well sample plate to allow for ease of use and multichannel pipetting of tubed index primers.

What does the plate fixture look like?

Is the plate fixture re-usable?

Yes, though it should be cleaned to prevent contamination, following lab cleaning best practices.

What is the catalog number?

FC-130-1005 (includes two fixtures).

How to order the plate fixture?

The plate fixture kit can be ordered via quote or by adding the catalog number via quick cart in MyIllumina.

Illumina has launched the Illumina DNA/RNA UD Indexes and the Illumina RNA UD Indexes, replacements to the IDT for Illumina DNA/RNA UD Indexes and the IDT for Illumina RNA UD Indexes, respectively. The latter will be obsolesced and have a last order date of January 30, 2025. Note the “IDT for” branding is removed in the newer products.

Some of the indexes have been versioned to improve consistency and performance. Illumina has also optimized the placement to improve color balance.

Sequence Updates The complete list of adapter sequences are provided in the updated Illumina Adapter Sequences Document #1000000002694. Indexes updated in the Illumina DNA/RNA UD Indexes kits will use the listed “v3” sequences where listed, and the “v2” sequences of UDP0252, UDP0258, UDP0289, UDP0290, UDP0291, and UDP0301. Please note, some “v2” index sequences have been moved to other plates to generate the “v3” indexes. (In contrast, IDT for Illumina DNA/RNA UD Indexes use “v2” sequences, where listed).

Plate Layouts Plate layouts are provided in the Index Adapters Pooling Guide # 1000000041074.

Usage Notes

• Due to the relocation of some indexes across plates, Illumina does not recommend combining IDT for Illumina DNA/RNA UD Indexes with the new Illumina DNA/RNA UD Indexes in the same run. This will avoid read misidentifications during sequencing analysis.

• BaseSpace Run Planning has been updated to include the new Illumina DNA/RNA UD Indexes and can produce Sample Sheets to export for use with BCL Convert software.

• New Library Prep kit and Index kit definition files for use with Local Run Manager v2 and Local Run Manager v3 are available on the Support page.

Catalog number changes

The IDT-ILMN RNA Index Anchors Box 96 (Catalog 20040899) subcomponent has not changed or been updated in the new Illumina RNA UD Indexes Set A-D, Ligation (96 Indexes, 96 Samples) (Catalogs 20091655, 20091657, 20091659, and 20091661).

Compatible Library Prep Kits

For any questions, contact Illumina Technical Support

The Sequencing Methods Explorer can be used to explore cutting-edge experimental next-generation sequencing (NGS) library preparation methods compiled from scientific literature. New methods will be continuously added.

Illumina has not tested or validated all methods. As such, users may have to consult the literature and validate the method in lab. Results of non-Illumina methods are not guaranteed, and these workflows are not supported by Illumina.

The following tables depicts the plate layout for Illumina DNA/RNA UD Indexes (v3), which are designed for dual-indexing.

The Index Adapters Pooling Guide, linked here, contains these tables along with recommended index combinations for low-plexity library pooling.

The product page for Illumina DNA Prep with Enrichment (S) Tagmentation is linked here.

• The product page includes the list of all relevant products to the library preparation workflow, including index kits and optional accessories.

The support page for Illumina DNA Prep with Enrichment (S) Tagmentation is linked here.

• The support page includes the reference guide (protocol), information on consumables and storage, links to frequently asked questions, support files, and additional helpful information.

This library prep kit was previously named Nextera Flex for Enrichment.

The product page for Illumina RNA Prep with Enrichment, (L) Tagmentation is linked here.

• The product page includes the list of all relevant products to the library preparation workflow, including index kits and optional accessories.

The support page for Illumina RNA Prep with Enrichment, (L) Tagmentation is linked here.

• The support page includes the reference guide (protocol), information on consumables and storage, links to frequently asked questions, support files, and additional helpful information

Note: the TruSeq DNA Exome library preparation kit has been discontinued. The following is provided just for reference. The product page for TruSeq DNA Exome is no longer available.

The support page for TruSeq DNA Exome is linked here.

• The support page includes the reference guide (protocol), information on consumables and storage, links to frequently asked questions, support files, and additional helpful information.

Note that this kit was previously named TruSeq Exome Library Prep Kit.

Note: the TruSeq Methyl Capture EPIC library preparation kit has been discontinued. The following is provided just for reference. The product page for TruSeq Methyl Capture EPIC is no longer available.

The support page for TruSeq Methyl Capture EPIC is linked here.

• The support page includes the reference guide (protocol), information on consumables and storage, links to frequently asked questions, support files, and additional helpful information.

The TruSight Cancer enrichment panel can be used with either TruSight Rapid Capture or Illumina DNA Prep with Enrichment library preparation reagents. This article provides direct links to the TruSight Cancer panel bundled with TruSight Rapid Capture.

The product page for TruSight Cancer bundled with TruSight Rapid Capture is linked here.

• The product page includes the list of all relevant products to the library preparation workflow, including index kits and optional accessories.

• Note that the TruSight Cancer MiniSeq kit (20005612) is bundled with TruSight Rapid Capture library preparation reagents.

The support page for TruSight Cancer bundled with TruSight Rapid Capture is linked here.

• The support page includes the reference guide (protocol), information on consumables and storage, links to frequently asked questions, support files, and additional helpful information.

• Note that this support page provides a link to the reference guide for preparing the TruSight Cancer panel with TruSight Rapid Capture library preparation reagents.

The product page for TruSight Myeloid is linked here.

• The product page includes the list of all relevant products to the library preparation workflow, including index kits and optional accessories.

The support page for TruSight Myeloid is linked here.

• The support page includes the reference guide (protocol), information on consumables and storage, links to frequently asked questions, support files, and additional helpful information.

Should index reads be performed if only one library is being sequenced in a run?

Illumina does not recommend performing index reads when one library is sequenced alone, as the index read(s) will be low in base diversity and this can negatively impact the sequencing performance, and can, in some instances, lead to run failure. If the run includes the single library and phiX, the phiX reads will be removed at the data alignment step. Alternatively, reads aligning to phiX can be bioinformatically removed prior to analysis of sample data.

• Note: phiX is an unindexed library and cannot be used to add base diversity to index reads.

When sequencing a single library in a run, it is not recommended to perform index reads, as the index read or reads will not be color balanced due to the presence of a single sequence.

• During run setup or when creating a sample sheet in Illumina Experiment Manager or Local Run Manager, enter zero for the index reads.

• All reads will go to the undetermined folder. Sample reads will be separated from PhiX reads (if present) during alignment in the analysis workflow.

Illumina sequencing reagent cartridges contain sequencing primer cocktails that allow for compatibility with Illumina's library preparation portfolio. The sequences of all sequencing primers are proprietary.

A complete list of Illumina's publicly available adapter and index sequences are available in the Illumina Adapter Sequences document.

What are the index sequences included in the AmpliSeq CD Indexes Large Volume kit for Illumina (96 Indexes, 96 Samples), catalog number 20019108?

The index sequences in the AmpliSeq CD Indexes Large Volume kit for Illumina are the same as the indexes for AmpliSeq CD Indexes Set A for Illumina, catalog number 20019105.

Link to Index Sequences

Link to Index Plate Layout

A few Illumina library prep kits have a single letter in parentheses as part of the library prep kit name:

• Illumina DNA Prep with Enrichment, (S) Tagmentation

• Illumina DNA Prep, (M) Tagmentation

• Illumina RNA Prep with Enrichment, (L) Tagmentation

These letters refer to the general size of the resultant library fragment post-tagmentation. S stands for "small," M for "medium," and L for "large" insert sizes.

Reagent composition and concentrations are proprietary; Illumina support is not able to access or share this information.

Index adapters and primers are supplied at the correct working concentration for use in compatible Illumina library preparation protocols. See the relevant library preparation reference guide for for determining the volume of adapters or primers to use.

A single-indexed library has only 1 index, specifically in the p7-side adapter. This is called the i7 index and is sequenced during index read 1 of the sequencing run. A single-indexed library must have the index in the p7 adapter to sequence on Illumina instruments.

A dual-indexed library has 2 indexes, index1 (i7) in the p7-side adapter and index2 (i5) in the p5-side adapter. Dual-indexed libraries can either be combinatorial dual (CD) or unique dual (UD). This concept is explained in Understanding unique dual indexes (UDI) and associated library prep kits

Note: On Illumina instruments, it is not possible to sequence an i5 index without first sequencing the i7 index (ie, a single-indexed run only sequencing the i5 index is not possible).

What is the minimum library size that can be sequenced?

If a fragment has complete adapter sequences, it can bind and cluster. The shortest Illumina library type is TruSeq small RNA libraries, which have ~20 bp inserts. Further, adapter dimers, with no inserts but with the complete adapter sequences, are about 120-150 bp and can cluster and sequence.

The Illumina Adapter Sequences Document contains the sequences of all Illumina indexes. The plate layouts/well positions for pre-plated indexes are in the Index Adapters Pooling Guide.

Illumina recommends creating sample sheets in Illumina Experiment Manager (IEM) or setting up runs in Local Run Manager (LRM), BaseSpace Run Planning, or BaseSpace PrepTab depending on the instrument and control software version.

The reference sequence used for PhiX alignment can be found in the Illumina iGenomes page.

All Illumina sequencing instruments already have the phiX reference, so the above reference is not required for assessing phiX alignment rates in sequencing runs. The sequence is made available as a reference, if needed.

The following TruSeq index kits come in each respective format.

This information can be found in the Index Adapter Pooling Guide. Note that some of the above index kit offerings have been discontinued, though the full table is provided for informational purposes.

Illumina Experiment Manager (IEM) is compatible with Windows 7, Windows 10, and Windows 11.

Illumina Experiment Manager (IEM) is not compatible with Mac operating systems or Linux distributions.