Oligo Pool Design & QC Before Vendor Upload
Run sequence QC, check synthesis risk, and export vendor-ready files before you submit CRISPR libraries, NGS panels, gene assembly pools, or mutagenesis designs for synthesis.
Choose a calculator, check a sequence set, or prepare an order file through PCR Primer Workflow, Build Pool Architecture, Run Pool Pre-Order QC, CRISPR Guide QC Workflow, and Vendor Order Prep Workflow.
Calculations run in your browser by default. Dashboard History can store the full input snapshot when auto-save, session, or account history is enabled; Library saves and membership/API workflows can send sequence assets by design.
Start with the Workflow
Choose the path that matches the job, then open the calculator, QC page, or export tool at the right step.
PCR Primer Workflow
Tm, GC, hairpin, dimer, MW, and dilution checks for primer-pair ordering decisions.
Build Pool Architecture
Assemble inserts, adapters, barcodes, primers, and motifs before pool-scale QC.
Run Pool Pre-Order QC
Screen sequence quality, export passing rows, and prepare vendor formatting after review.
Estimate Synthesis Yield
Estimate full-length yield, truncation burden, and pool-scale error risk before ordering.
Plan Coverage Depth
Estimate library coverage, redundancy, and dropout risk for pooled experiments.
CRISPR Guide QC Workflow
Coverage planning, MOI scale, guide QC, synthesis fields, and stable CRISPR library order prep.
Vendor Order Prep Workflow
Vendor-specific IDT, Twist, GenScript, or Dynegene export after QC and vendor selection.
Pre-Order Checks for Oligo Pools
Check the sequence file before synthesis: clean formats, flag risky rows, estimate synthesis loss, and size the pool for the experiment.
Format Converter
Transform sequences between FASTA and CSV with strict validation rules.
Batch Sequence QC
Review up to 1,000 sequences free, or 50,000 with Tool Membership, for Tm spread, GC limits, homopolymers, and secondary-structure risk.
Error Rate & Uniformity
Estimate full-length yield, coupling efficiency effects, and representation risk before ordering.
Coverage Calculator
Estimate the material and coverage needed to reduce dropout in pooled experiments.
Built for High-Throughput Applications
Open focused guides for CRISPR libraries, NGS panels, and multiplex PCR primer sets.
CRISPR sgRNA Libraries
Plan sgRNA libraries with balanced guide sets, clean sequences, and fewer off-target risks.
NGS Target Enrichment
Design hybridization capture probes with balanced GC content for uniform enrichment.
Multiplex PCR Panels
Mitigate primer-dimer formation and Tm imbalances to ensure even amplification across hundreds of targets.
Why Use These Tools
Published Method Basis
Tm and related calculations reference peer-reviewed methods, including SantaLucia 1998 and Breslauer 1986, with assumptions documented in the method pages.
Browser Default Data Boundary
Calculations run in your browser by default. Dashboard History can store the full input snapshot when auto-save, session, or account history is enabled; Library saves and membership/API workflows can send sequence assets by design. Analytics records aggregate site interactions, not sequence content or result rows.
Open Free Tier
Use the calculators directly for quick checks without vendor lock-in. Member licenses extend high-volume batch and API workflows.
Workflow basis
Move from a sequence question to a checked result
OligoPool connects calculators, method notes, limitations, and reference paths so you can review a sequence set, understand the assumptions, and decide the next ordering or troubleshooting step.
Original tool workflow
The public surface is organized around sequence decisions researchers actually make: calculate Tm, check GC and structures, run pool-scale QC, convert vendor files, and keep method assumptions visible before ordering.
Published method trail
Calculator pages route into method references, accuracy notes, salt-correction comparisons, and limitation text instead of asking users to trust a black-box result.
Transparent site boundaries
The site separates browser-default public calculations from optional account, library, membership, API, and admin surfaces, with privacy and terms pages linked from the public layout.
Vendor-Agnostic Order Preparation
Move from a checked sequence pool to a vendor shortlist and export format. Compare pool fit, QC scope, delivery assumptions, and file requirements before ordering.
Open the Oligo Pool GuideCompare pool vendorsHow We Compare
Compare common oligo analysis tools by methods, inputs, privacy model, and batch support.
Start with the Right Calculator
Browse all available tools or open the relevant guide before checking a sequence set. The free tier requires no registration; member limits use an active license. For common experimental contexts, see the use case examples and related design notes.
Built for research use
What is an Oligo Pool?
An oligo pool is a complex mixture of thousands to millions of distinct single-stranded DNA oligonucleotides synthesized in parallel on a microarray surface. Unlike traditional column-based synthesis which produces individual oligos in separate tubes, microarray synthesis generates massive libraries of sequences simultaneously in a single pool.
Parallel synthesis makes large sequence libraries practical for functional genomics. Oligo pools support high-throughput applications such as designing CRISPR sgRNA pools for pooled screening, assembling synthetic genes from oligo pools, and building custom NGS target-enrichment panels.
Due to the inherent constraints of parallel synthesis, such as varying coupling efficiencies and edge effects on the microarray, computational quality control is critical. Predicting error rates and ensuring uniform sequence representation before ordering your pool can prevent costly experimental failures downstream.