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Illumina libraries: large projects

We developed custom, high-throughput protocols to make sequencing of a large number of samples affordable to all.

Our custom protocols have been internally validated, and used for several years. They yield an average success rate of 90%.

If you have a large project but you would rather use the commercial kits, let us know.

Prep kits for DNA-Seq

  • TruSeq-equivalent

    We use a homemade mix that uses the same ligase as the commercial TruSeq Illumina kit. Our method yields comparable results to the commercial kit, but it is more cost-effective. Offering a full coverage of the genome, the TruSeq-equivalent protocol can be used to sequence organisms that do not have a reference genome. This method can be used for PCR-free sequencing.
  • Nextera (Illumina) skim sequencing

    Relying on the commercial Nextera kit, we save on reagent cost by using high dilutions (up to 3072-plex). We can also prepare the library in a lower volume, using less reagent and further decreasing the overall price of the library. This method is very cost-effective but yields a low coverage. We recommend it to sequence a very large number of samples for which high-level patterns of diversity are needed. It's not recommended for genomes that do not have a reference genome. This method cannot be used for PCR-free sequencing.
  • Nextera XT (Illumina)
    We use this commercial kit if you are working on organisms that have a small genome.

Prep kits for RNA-Seq

  • QuantSeq FWD (Lexogen)
    We use the Illumina-compatible, commercial kit developed by Lexogen as a cost-effective option for RNA-seq.

To be able to process large numbers of samples quickly, we will not carry out systematic QC on all the samples before the library preparation. You are responsible for providing samples that meet the quality standards we discuss with you during the project consultation.

Service pricing

Illumina libraries: large projects
DescriptionInternal price (Cornell and Cornell affiliates)External price
TruSeq-equivalent WGS library preps (custom protocol with PCR). Half plate, 48 samples* $3,136 5,143
TruSeq-equivalent WGS library preps (custom protocol with PCR). Full plate, 96 samples* $4,182 $6,859
Nextera skim sequencing WGS library preps (1/3 concentration). Half plate, 48 samples* $950 $1,559
Nextera skim sequencing WGS library preps (1/3 concentration). Full plate, 96 samples* $1,267 $1,559
Nextera XT small genome WGS library preps (full volume Illumina protocol). Half plate, 48 samples* $4,277 $7,014
Nextera XT small genome WGS library preps (full volume Illumina protocol). Full plate, 96 samples* $5,702 $9,352
Low-volume Nextera XT small genome WGS library preps (1/5 volume reactions). Half plate, 48 samples* $1,901 $3,117
Low-volume Nextera XT small genome WGS library preps (1/5 volume reactions). Full plate, 96 samples* $2,534 $4,156
3'RNAseq library preps. Quarter plate, 24 samples $1,639 $2,688
3'RNAseq library preps. Half plate, 48 samples* $2,186 $3,585
3'RNAseq library preps. Full plate, 96 samples* $2,915 $4,781
* These numbers include one blank well