TailorMix Dual-Indexed PhiX Control Library (Non-denatured)


Barcoded PhiX library for high quality NGS data without PhiX contamination.

For monitoring index-swapping in library pools.

Unit Content: 10nM non-denatured library in TE, 10uL


(previous SKU: TM-502-ND)

SKU: TM-580 Category:


SeqMatic’s TailorMix Dual-Indexed PhiX control library is a adapter ligated library used as a control for Illumina sequencing instruments. Our custom indexed library eliminates PhiX contamination in multiplexed sequencing runs, enabling the generation of cleaner raw data and the option to analyze the PhiX reads for quality control purposes such as monitor library barcode swapping. Each tube contains 10uL of double stranded library at a concentration of 10nM and can be used as a direct replacement for Illumina PhiX V3.


Positive Control Library for Illumina NGS

  • Compatible with all Illumina NGS systems including NovaSeq 6000, HiSeq 4000, HiSeq 2500, MiSeq and NextSeq
  • Data can be used for sequencing run quality control and index swap monitoring

High Flexibility

  • Positive control library used to monitor instrument error rates and read quality
  • High diversity library can be used to supplement low nucleotide diversity sequencing runs

Unique Dual-Index Barcodes

  • Custom designed dual-index sequences (can also be used in single index runs)
  • Compatible with all SeqMatic and Illumina sample prep kits
  • Additional barcode combinations available as custom orders

Easy to Use

  • Supplied as a double stranded 10nM stock in TE
  • Direct replacement for Illumina PhiX V3

Recommended For:

  • 16S amplicon sequencing
  • Single PCR amplicon sequencing
  • Viral genome sequencing
  • Low diversity libraries
  • Highly multiplexed pools
  • Single sample runs
  • Unindexed libraries


Sample Data:

PhiX Data

Figure 1: Percentage of sequencing reads mapping to the PhiX 174 genome using Indexed PhiX compared against Illumina PhiX V3.


Customer Testimonials:

“PhiX contamination in our data used to be a significant issue given that we were sequencing viral DNA extracted from patient biopsies.  We no longer see PhiX contamination with your product, which ultimately streamlines our data processing and gives us additional peace-of-mind regarding the validity of our data.”

Eric Sherman
University of Pennsylvania


“My lab was noticing large amounts of bleed-through of Illumina’s PhiX v3 into our indexed samples. Seqmatic’s Indexed PhiX dramatically reduces this bleed-through and allows us to estimate our incidence of sequencing crossover contamination.”

Customer C.F.
San Francisco, CA


Citations & References:

Shechner, David M., et al. “Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display.Nature methods 12.7 (2015): 664-670.

Additional information

Weight 0.5 lbs
Dimensions 4 × 6 × 0.5 in

Product Support

User Guide:

User Guide (PDF): Updated March 2018

Sample Sheet Setup

The TailorMix Indexed PhiX control library contains dual indexed barcodes which can be demultiplexed with all Illumina compatible demultiplexing software.

The TailorMix Dual-Indexed PhiX control library contains dual-indexed barcodes which can be demultiplexed with all Illumina compatible demultiplexing software. To monitor the percentage of PhiX reads in a sequencing run, include the TailorMix Dual-Indexed PhiX barcodes on the sequencing Sample Sheet for demultiplexing.

If the TailorMix Dual-Indexed PhiX barcodes are not included on the sequencing Sample Sheet, the PhiX reads will be parsed into a folder named “Unknown” or “Undetermined” along with any other reads with index sequences not defined in your sample sheet.

For individual downstream analysis of the Dual-Indexed PhiX library, your sample sheet can be modified to parse the PhiX reads into its own individual set of files. Simply add a new line to your sample sheet file containing the sequences below as your index barcodes. For single index read sequencing runs, only use the i7 Index 1 barcode sequence. The sequence length may also be adjusted as necessary to match the length of the index read.

i7 Index 1 barcode: TCGAATGA
i5 Index 2 barcode for MiSeq and HiSeq 2000/2500: GACATGCG
i5 Index 2 barcode for MiniSeq and NextSeq: CGCATGTC

Input Recommendations

Note: Optimal ratio of Dual-Indexed PhiX control library in the sequencing run could be different for each amplicon library.

Library Type Input Recommendation
  • TruSeq DNA or RNA
  • Nextera or ScriptSeq
  • TailorMix DNA or RNA
1% of final loading concentration
  • TruSeq Small RNA
  • TailorMix miRNA
5-10% of final loading concentration
  • PCR Amplicons (e.g. 16S, ITS, etc.)
15-25% of final loading concentration
  • Control Lane
  • PhiX Only Run
100% of final loading concentration


Storage Recommendations

The TailorMix Dual-Indexed PhiX Control Library is stable when stored at -20°C. Storage at -80°C has shown improved stability and is recommended for long term storage.

Best Practices

• Do not store the TailorMix Dual-Indexed PhiX Control Library in frost-free freezers.
• Aliquots should be made to allow for use to minimize repeated freeze/thaw cycles.
• Determine the appropriate aliquot volume based on usage.
• Aliquots that are in use can be stable for up to one month if kept on ice at all times during use and stored at temperature of -20°C or lower when not in use.

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