Direct Ordering lets you submit gene fragment orders to Twist Bioscience without leaving Benchling. You can select sequences from your Notebook, run manufacturability checks, configure your order, and place the order all from a Canvas app embedded in your Notebook entry. The synthesized DNA ships to your lab and links back to the sequences and project record they originated from. This article covers how to place a gene fragment order using the Twist Bioscience ordering app.

Who this is for: Scientists ordering gene fragments from Twist Bioscience as part of their Benchling workflow.

What you can do today:

• Submit one sequence at a time, or a worklist of sequences
• Get feasibility, complexity, and pricing from Twist before ordering
• Select delivery format (tube or plate), buffer, normalization, capping, and shipping address
• Pay with a Twist blanket PO
• Download a quote PDF and order confirmation

Before you start

You will need:

• The Twist Gene Fragments app installed on your tenant. If you do not see the app available, contact your Benchling POC
• A Twist account, using the same email address as your Benchling account. The Twist Gene Fragments app authenticates you as the individual placing the order, so the email on both accounts must match
• At least one shipping address configured in your Twist account. The app pulls shipping addresses from Twist; if none are set up, you will see a warning during checkout
• A blanket PO with Twist for payment. If your team uses a different payment method, contact your Benchling POC

Understand sequence requirements

Twist gene fragments have specific manufacturing constraints. Review these before submitting sequences.

• Sequence length: 300 bp to 1,800 bp (standard); 200 bp to 3,000+ bp with modifications
• Sequence content: DNA nucleotides only, no degenerate bases
• GC content: Ideally 25–65%. Sequences outside this range may receive warnings or be excluded
• Construct name length: 35 characters maximum. Names longer than 35 characters are auto-truncated. If names duplicate after truncation, an index will be appended (for example, _1, _2).
• Homopolymer runs: Long repeats (e.g., poly-A greater than 20 bp) may be flagged

If a sequence doesn't meet Twist's manufacturability criteria, the app displays a warning during the scoring step. Non-manufacturable sequences are excluded from the order.

Place an order

Insert the canvas and select sequences

The Twist Bioscience ordering app is a Canvas app that lives inside your Notebook entry. You can insert it into any Notebook entry, it's not limited to a specific template. The Canvas persists in your entry even if you navigate away. Your progress is saved if you close the tab and return.

1. Navigate to your notebook entry
2. Click the insert dropdown and select Twist App Canvas
3. The app opens in a Canvas panel within your entry
4. Select your sequences, which you can do via one of the three options below. You may only use one input method per order
   • Search for individual sequences
     • Use the Search for DNA Sequences field to select an existing DNA sequence from the Benchling Registry and add one at a time 
   • From a worklist
     • Use the Or select a Worklist field to use an existing Benchling worklist containing your DNA sequences
     • If the app can't access your worklist, go to the worklist settings and add the app as a collaborator
     • Worklists accept unique sequences only. If you need the same sequence in multiple positions, this is not supported in the current release.
   • By pasting raw nucleotide strings
     • Use the Or add sequences as nucleotide strings section to paste sequences directly (for example, copied from a CSV or external tool). For each sequence: 
       • Enter a name in Sequence Name
       • Paste the nucleotides into Sequence Nucleotides
       • Use Add Rows to add more sequences, or Clear All to start over 
5. Once your sequences are loaded, click Analyze Sequences

Note: If your team generates sequences programmatically, you can register them via the Benchling API, create a worklist, and share the worklist with the app before using the Canvas to order.

Select adapter preference 

Below the input section, set the Adapters dropdown. The app defaults to No (without adapters). Change to Yes if you want to order with adapters.

Authenticate to Twist 

On your first use, the app prompts you to authenticate with your Twist account.

1. Once you click Analyze Sequences, the app displays an Authentication Required message
2. Click the Twist account authentication link
3. Sign in with the email that matches your Benchling account and your Twist password
4. Once you see Authentication successful!, navigate back to your Canvas in Benchling
5. Click Analyze Sequences again to proceed

Note: If the login window doesn't appear, check that pop-ups are enabled in your browser. If authentication fails, confirm your Twist account is active and that your organization has authorized the Benchling integration.

Analyze sequences

Click Analyze Sequences. The app sends the sequences to Twist's API and shows Analyzing sequences for feasibility… while it works.

Note: When the Canvas is processing an API call, it pauses briefly. This is normal, if it remains frozen for more than 5-10 minutes, reload the Notebook entry or contact Benchling Support. 

Review & Pricing 

The Review & Pricing page shows a table of every sequence with its analysis results:

• Name — your Benchling sequence name (truncated to 35 characters if longer)
• Sequence — first nucleotides of the sequence
• BP — number of base pairs
• GC % — overall GC content
• Complexity Score — Standard, Complex, or Not Accepted
• Price (USD) — based on your Twist contract
• Feasibility — green dot (feasible) or red dot (infeasible)
  • Green (feasible): The sequence passes Twist's complexity check and can be ordered
  • Red (infeasible): The sequence can't be manufactured as submitted. The app shows the reason (e.g., sequence too short, homopolymer issues). These sequences are automatically excluded from the order. To order infeasible sequences, contact customersupport@twistbioscience.com. To make the sequence feasible, edit it in Benchling and re-run the analysis

Below the table, the Warnings & Errors section shows a count of warnings and errors. Each warning lists the sequence name and a description, such as high GC content, repeat density, repeat regions, or homopolymer stretches.

1. Click Show Issues to expand the full list
2. When you are ready, click Continue → to move to order settings. You can only proceed with manufacturable sequences

Note: A sequence with warnings can still be ordered. To resolve a warning, edit the sequence in Benchling (for example, using codon optimization tools) and re-run the analysis.

Configure your order 

The configuration flow walks through five settings, one screen at a time. Each screen shows your progress at the top: completed selections have a green checkmark, the current step has a blue arrow, and upcoming steps show an hourglass.

• Screen 1: Delivery Format Choose how Twist ships your DNA. Options shown reflect what Twist currently offers
  • Note: plates are filled By Column. Custom plate maps that assign specific sequences to specific wells are not supported in the current release 
• Screen 2: Shipment
• Screen 3: Buffer
• Screen 4: Normalization
• Screen 5: Capping Capping is only available when Normalization is set to No
  • When normalization is set to Yes, capping is skipped automatically

Review the order summary and request a quote

The Order Summary page displays every selection you made: Delivery Format, Shipment, Buffer, Normalization, and Capping. Review them carefully, if you need to change anything, use the Back button.

Under Shipping Address, you will see the addresses configured on your Twist account. Click Use next to the address you want.

When you are ready, click Request Quote → to retrieve final pricing from Twist.

Checkout & order confirmation

The Checkout page shows:

• Order Summary — repeats your selections
• Pricing Breakdown — Item Subtotal, Shipping, Handling, and Total Cost. Detailed line items break out price by sequence length band (e.g. 300bp–500bp, 501bp–1800bp).
• Download Quote PDF — click to download a PDF of the quote
• Payment Method — your blanket POs from Twist

Click Use next to the blanket PO you want to use, then click 🛒 Place Order Now.

After placing the order, the Canvas shows the Order Confirmation page with:

• Quote Number (for example, Q-451959)
• Status (ORDER_CREATED)
• Order Total
• Payment method
• Full order details
• What Happens Next? — production timeline (2–4 business days), including queuing, manufacturing and QC, and shipping
• Contact information for Twist customer support
• You will receive — list of expected communications:
  • Order confirmation email (within 1 hour)
  • Production updates (weekly)
  • Shipping notifications (when ready)
  • Final delivery confirmation

Save your Quote Number for future reference. The Canvas persists in your notebook entry, so you can return to the confirmation any time.

After you order

• Order status, shipment tracking, and updates happen in Twist. You will receive email updates from Twist about production, QC, and shipment status. The Twist app does not currently surface these updates inside Benchling
• The Canvas persists in your notebook entry. You can revisit your order configuration and confirmation any time, as long as you do not delete the Canvas
• To place another order, insert a new Canvas in a notebook entry. Each order is tracked independently.
• Returned DNA preps are not automatically registered in Benchling in this release. Register preps using your existing process when the order arrives

Frequently asked questions

Q: Can I order the same sequence in multiple positions in a plate? 

A: Not in this release. Worklists accept unique sequences only, and custom plate maps are not supported.

Q: Can I order clonal genes or antibodies? 

A: Not through this app today. The current release supports linear DNA (gene fragments) only.

Q: Can I upload a custom plate map? 

A: Not in this release. If you select a plate delivery format, sequences fill the plate By Column in the order Twist receives them.

Q: How do I order without adapters? 

A: The Adapters dropdown on the Linear DNA Ordering page defaults to No. Change it to Yes if you want to order with adapters.

Q: Can I export a list of sequences that failed feasibility? 

A: Not in this release. If your worklist contains many failures, you will need to scroll through the analysis table to identify them.

Q: Can I order an infeasible sequence anyway? 

A: Not through the app. The app excludes infeasible sequences from the order automatically. Contact Twist customer support at customersupport@twistbioscience.com to discuss exceptions.

Q: How long does authentication last? 

A: Authentication lasts a few days. You will not need to re-authenticate for every order.

Q: Why did the Canvas freeze? 

A: The Canvas pauses while it makes API calls to Twist. This is normal. Give it 5–10 minutes. If it does not recover, reload the notebook entry or contact Benchling Support.

Q: My sequence name was truncated. Why? 

A: Twist construct names are limited to 35 characters. Names longer than that are truncated. If two truncated names match, the app appends an index (_1, _2).

Q: Where do I find the construct name Twist will use? 

A: The Name column on the Review & Pricing page shows the name as it will be submitted to Twist, after any truncation or indexing.

Q: Who do I contact for help?

• Order, pricing, or Twist account issues: customersupport@twistbioscience.com
• Benchling app or interface issues: support@benchling.com