Library / Automated NGS Library Prep

Automated NGS Library Prep

Fragmentation through dual-sided size selection — executed hands-free on your existing bench, with vision checks on the bead steps that usually break.

Simulated Genomics ⏱ ~3h walk-away Advanced Accuris AutoMATE 96 96 samples

Why automate this

Manual NGS library prep is the throughput ceiling in most sequencing cores. A single 96-sample batch involves several hundred precise pipetting steps and multiple SPRI bead cleanups — and one missed wash, one over-dried bead pellet, or one mis-indexed well costs a sample and a sequencing slot. It's also the step most likely to introduce batch effects, because hand pipetting varies run to run and technician to technician.

This protocol runs the entire workflow on the Undergrad and vision-verifies the error-prone bead steps in real time, so library-to-library consistency improves and failures are caught at the bench instead of at the Bioanalyzer or — worse — on the sequencer.

Workflow at a glance

Input QC & normalize→ Fragment / tagment→ End repair & A-tailing→ Adapter ligation→ Post-ligation SPRI→ Indexing PCR→ Dual-sided size selection→ Final QC

Who it's for

Sequencing cores and translational labs running library prep regularly (roughly a plate a week or more) that are bottlenecked on hands-on time and want reproducible, audit-ready libraries without hiring more technicians or buying a dedicated NGS automation suite.

The four-layer architecture at a glance

Four-layer architecture diagram for Automated NGS Library Prep: intent, semantic workflow, robot actions, and atomic actions.
Intent → semantic workflow → robot actions → atomic actions — every stage runs through the same four layers on the Undergrad.

In this protocol

① Setup → instruments, reagents, input requirements & deck layout ② Steps → the full workflow with volumes & timings ③ Results → QC metrics & what good looks like ④ Troubleshooting → failure modes, fixes & when not to automate