We prepare next-generation sequencing libraries using standard, validated protocols, scaled to fit projects of any size — from a handful of samples to full-plate, high-throughput runs.

Overview

Library preparation is available at two scales. Low-Throughput prep is fully manual and best for individual samples or small batches, with a success rate near 100% — any sample that fails on the first attempt is repeated at no additional charge. High-throughput prep is optimized for large sample sets processed in 96-well plates, with an average success rate of 90%. Both scales use the same underlying chemistries described below.

We strongly recommend unique dual indices (UDIs) for sample multiplexing; a set of 384 (4 x 96) UDIs are available for both tagmentation and ligation methods. For projects needing higher levels of multiplexing, combinatorial dual indexing can support thousands of samples per sequencing run, though it carries a higher risk of index hopping on patterned flow cells.

DNA Library Preparation

Tagmentation

A fast, enzyme-based method well suited to large or complex genomes, microbiome samples, and metagenomic samples. Several options are available:

• Standard prep — our default tagmentation protocol for individual samples or small batches.
• Full volume (plate-based) — the same chemistry as the standard prep, run at larger scale and lower per-sample cost.
• Low volume — a reduced-volume reaction that lowers cost further but requires a minimum of 47 samples per run to yield enough final library for sequencing.
• Skim sequencing — uses a diluted tagmentation enzyme for a very cost-effective, low-coverage library. Best for very large sample numbers where other genomic resources (e.g., haplotype maps) are already available; not recommended without a reference genome.

Ligation (TruSeq)

Offers full, even coverage of the genome and is the better choice when a reference genome is not available. The standard protocol uses PCR to incorporate UDIs (up to 384 available). A PCR-free version is also offered, with more limited indexing (up to 96 samples with UDIs) and requires digital PCR for quantification prior to pooling.

RNA Library Preparation

Full-service RNA sequencing and small RNA sequencing are available for standard-scale projects, and a cost-effective 3'-tag method is available for large sample sets.

Standard RNA-seq & Small RNA Sequencing

Full-transcript RNA-seq and small RNA sequencing packages, prepared individually for standard-scale projects.

• RNA-Seq Standard package
• Small RNA Sequencing Standard Package

3' RNA-seq (High-Throughput)

A cost-effective alternative to full-transcript RNA-seq that captures only the 3' end of each mRNA, with one read per transcript. We strongly recommend confirming RNA quality before submitting samples (determining RNA sample concentrations and quality (integrity) will incur additional charges). Individual libraries are quantified and pooled for sequencing as part of the service; analysis is not included but may be available through the Bioinformatics Facility.