Automated Design of Oligopools and Rapid Analysis of Massively Parallel Barcoded Measurements.

ABSTRACT: Oligopool synthesis and next-generation sequencing enable the construction and characterization of large libraries of designed genetic parts and systems. As library sizes grow, it becomes computationally challenging to optimally design large numbers of primer binding sites, barcode sequences, and overlap regions to obtain efficient assemblies and precise measurements. We present the Oligopool Calculator, an end-to-end suite of algorithms and data structures that rapidly designs many thousands of oligonucleotides within an oligopool and rapidly analyzes many billions of barcoded sequencing reads. We introduce several novel concepts that greatly increase the design and analysis throughput, including orthogonally symmetric barcode design, adaptive decision trees for primer design, a Scry barc

SUBMITTER: Hossain A 

PROVIDER: S-EPMC11669329 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature