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Cornell University

Illumina libraries: large projects

We have 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 also be used as a PCR-free prep.
  • Nextera (Illumina) Skim sequencing

    These library preparations use standard Illumina Nextera kits with a diluted tagmentation enzyme (1/3 concentration). Large numbers of samples (up to 3072-plex) can be pooled for a single sequencing run. This method is very cost-effective but yields a low coverage. We recommend it for sequencing a very large number of samples for which other genomic resources are available (e.g. haplotype maps). It's not recommended for genomes that do not have a reference genome. This method cannot be used as a PCR-free prep.
  • Nextera (Illumina) — Low volume
    These library preparations use standard Illumina Nextera kits with reaction volumes reduced from 50uL to 10uL per library (1/5 volume); the ratio of DNA to tagmentation reagents is maintained. Because the library volume is low, you must submit at least 48 samples to have enough library volume for sequencing. This method cannot be used as a PCR-free prep.
  • Nextera Flex (Illumina) — Full volume

    These library preparations use standard Illumina Nextera Flex kits for any number of samples, and offers a wide range of input concentrations. This method cannot be used as a PCR-free prep.

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 only QC a subset of samples (see pipeline). We do not carry systematic QC on all your 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
Skim sequencing Nextera WGS library preps (1/3 concentration). Half plate, 48 samples* $950 $1,559
Skim sequencing Nextera WGS library preps (1/3 concentration). Full plate, 96 samples* $1,267 $2,078
Low volume Nextera WGS library preps (1/5 volume). Half plate, 48 samples* $3,029 $3,117
Low volume Nextera WGS library preps (1/5 volume). Full plate, 96 samples* $3,207 $4,156
Full volume Nextera WGS library preps. Half plate, 48 samples* $4,498 $7,014
Full volume Nextera WGS library preps. Full plate, 96 samples* $6,144 $9,352
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