Last updated: April 21, 2026

How to Order an Oligo Pool

Use this guide when your sequences are ready and you need to submit an order without format or capacity mistakes. It covers accepted file formats, ID rules, vendor capacity limits, modification notes, and the final checklist before you place an oligo pool order.

Before You Submit the File

This page handles the submission step. If the design, QC expectations, or vendor shortlist are still open, start with the main oligo pool guide and the decision pages below before using the file-format checklist.

Start With the Oligo Pool Guide

Confirm the concept, design path, synthesis route, and application fit.

Read QC Metrics First

Set expectations for uniformity, dropout, error rate, Gini, and NGS verification.

Compare Pool Vendors

Short-list vendors by public specs, QC language, turnaround, and service boundaries.

High-throughput oligo pool synthesis facility

Automated oligo pool synthesis array preparing large-scale orders.

Accepted File Formats

FormatExtensionTwistAgilentIDTGenScriptNotes
FASTA.fasta, .fa✅✅✅✅Most universal format
CSV.csv✅✅✅✅Columns: Name, Sequence
TSV.tsv✅⚠️✅✅Tab-separated variant of CSV
Excel.xlsx✅❌⚠️⚠️Twist-preferred for large orders
Plain Text.txt⚠️⚠️⚠️⚠️One sequence per line (no IDs)

Use our Format Adapter to convert between formats and validate before submission.

Sequence ID Naming Rules

✅ Good IDs

  • BRCA1_sgRNA_01
  • TP53_exon5_probe_001
  • GFP_tile_15_of_30
  • NTC_control_0001

❌ Bad IDs

  • seq 1 (spaces)
  • BRCA1/sgRNA#1 (special chars)
  • 1_oligo (starts with number)
  • duplicate_name (non-unique)
Rules: Alphanumeric + underscores only. Start with a letter. Must be unique. Max 50 characters. No spaces or special characters.

Order Specifications by Vendor

SpecificationTwist BioscienceAgilent SurePrintIDT oPoolsGenScript GenTitan
Min Pool Size2,000 oligos5,000-10,000100 oligosContact vendor
Max Pool SizeNo stated limitUp to 244K/chip20,000 (1 pmol)Up to 8M/chip
Min Length20 nt60 nt21 nt20 nt
Max Length300 nt230 nt350 nt170 nt
Delivery FormatLyophilized (tube)LyophilizedLyophilizedLyophilized
Yield/Oligo1-10 pmol~10 fmol1/10/50 pmol tiersVariable
Turnaround2-4 business days3-6 business daysContact vendor3-5 business days
Rush OptionContact salesContact salesContact salesContact sales
ModificationsBiotin, phosphoBiotinBiotin, phosphoBiotin, phospho, amino

Use this table as a submission screen, then confirm the current quote, QC package, and service terms directly with the vendor. For source-backed public specs, open the 2026 vendor specs snapshot. For decision support, see the oligo pool vendor comparison.

Submission Checklist Before You Order

  • □All sequences pass Batch QC (no extreme GC, homopolymers, strong hairpins)
  • □Sequence IDs are unique, alphanumeric + underscores only
  • □File format matches vendor requirements (FASTA recommended)
  • □Pool size within vendor capacity limits
  • □All oligos within vendor length limits
  • □Controls included (1K non-targeting for CRISPR, WT for mutagenesis)
  • □Modifications specified (biotin for capture, none for standard)
  • □Budget approved (estimate cost before requesting quotes)
  • □NGS QC requested (included by Twist/IDT, add-on for Agilent)

Frequently Asked Questions

What file format do I need for an oligo pool order?▾
Most vendors accept FASTA (.fasta, .fa) and CSV/TSV (.csv, .tsv). FASTA is the most universal: >unique_id followed by the sequence on the next line. Some vendors (Twist) also accept Excel (.xlsx). Use our Format Adapter to convert between formats.
What is the minimum order size for an oligo pool?▾
Twist: 2,000 oligos minimum. Agilent: typically 5K-10K oligos. IDT oPools: 100 oligos minimum. GenScript: contact vendor. Below 1K oligos, consider ordering individual oligos instead — the per-oligo cost advantage of pools diminishes at small scales.
How much DNA do I receive from an oligo pool order?▾
Varies by vendor: Twist delivers 1-10 pmol per oligo (lyophilized). Agilent: ~10 fmol per feature. IDT: normalized per-oligo yield. GenScript: variable. All pools require PCR amplification before use — the delivered amount is a starting template, not a working stock.
Can I get sub-pools (multiple pools in one order)?▾
Twist Bioscience supports up to 100 sub-pools per order, selectively amplifiable with unique primer pairs. This is ideal for multi-experiment designs or dose-response studies. Not all vendors support sub-pooling.

Next Pages to Open

Design an Oligo Pool Before Ordering

Use the five-step checklist before you send sequences out.

Review Oligo Pool Design Rules

Check sequence constraints before your file is rejected or underperforms.

Compare Oligo Pool Vendors

Match submission requirements, QC, and turnaround across vendors.

Estimate Oligo Pool Cost

Estimate pricing before you finalize a vendor choice.

Convert Vendor File Formats

Convert between FASTA, CSV, and vendor-ready formats.

Run Batch QC Before Submission

Screen sequences before they reach a vendor quote or order form.