PoolMate

Pool libraries into one tube. Enter your samples, then use the actions at the bottom: Calculate molarities (quick nM check) · Quick pool table (manual pooling, no robot files) · Generate worklists (full epMotion DNA + Buffer export).

Run metadata

Run name

Operator

Kit lot

Instrument / method

Notes

Create pool parameters

Platform

Loading preset

Pool calculation mode*

Target pool nM*Use when your SOP defines a final pool concentration.

Total final volume µL*

Layout*

Optional extra pooling parameters

Minimum transfer µL

Round transfer to µL

Dead volume / excess %

Source rack number

Destination rack number

Buffer rack numberUsually the same as the source rack. Only change it if your epMotion method has a dedicated buffer position on another rack (many fixed pooling scripts only use racks 1–2).

Buffer source position

Pool well

Low-volume handling

Pre-dilution final volume µL

Pre-dilution safety margin %

Tip policy

Max well capacity µL

Dilution rack number

Dilution starting well

These fields have safe defaults. Leaving this section closed does not block worklist generation.

Minimum for Generate Worklists: sample molarities plus pool mode, total final volume, and layout. Use nM mode for Illumina-style final concentration. Use fmol mode for ONT-style total load.

Quick pool method

What this does

Creates a simple manual pooling table from the Sample section without requiring platform presets, deck settings, destination racks, buffer positions, or epMotion worklist exports.

Minimum required: sample molarity inputs plus either fmol per sample or total fmol pool. This is for quick bench calculations, not full robot execution.

Quick pool target

Quick pool mode*

fmol per sample*

Round transfer to µL

Outputs transfer volumes only — no epMotion files. Pick the target style that matches your SOP: fmol per sample, total fmol, an Illumina-style target nM in a final volume, or simply an equal volume from every sample.

Samples

Shared fragment size (bp), optional

Default input mode

This form starts blank each time the file is opened. Click Save run to keep your work as a file you can reopen — unsaved entries are cleared on the next open.

#	Source well	Name / number	Input mode*	Conc reads ng/µL*	Size bp*	Direct nM*	Out well

Samples entered0

Mass-mode samples0

Overall avg concentration-

Concentration range-

* Minimum for Calculate Molarities: either concentration reads + size bp, or direct nM. Sample names and source wells help with tracking but are auto-filled if left blank. For replicate Qubit reads, enter values separated by commas, semicolons, or spaces. The overall average concentration below is calculated across mass-mode samples only.

Pool preview

The preview follows your Layout choice: Tube shows source plate → pool tube, Plate shows source plate → output plate. Volumes appear once the pool target and total volume are set.

Add samples or source wells to preview the layout.

Normalize — dilute each library to a target concentration (plate → plate)

Enter each library's well and concentration. PoolMate dilutes each one to the target concentration in a separate output plate and exports Normalization_DNA.csv + Normalization_Buffer.csv for your Eppendorf normalization script: source plate (Rack 1) → output plate (Rack 1), buffer from the reservoir at position "1". Each output well defaults to the same well as its input — set Output well to move a library somewhere else (e.g. A3 → D5).

Concentration unit*

Target concentration*

Final volume per well µL*

Min transfer µL

Round to µL

Input well	Name	Concentration*	Output well

Target and each concentration must use the same unit. The target must be below every library's concentration (this dilutes, it can't concentrate).

Load — flow cell loading calculator

Platform*

Flow cell / kit preset

Target load fmol*

Min transfer µL

Round to µL

Pools to load

With several pools, Share sets the relative amount of each (all 1 = equal molar). Set 2 to give a pool twice the representation.

#	Pool name	Concentration*	Unit	Size bp	Share

Presets are starting points from the vendor documentation — always confirm against your own kit and instrument SOP.

Standalone dilution calculator

Dilute one sample or a whole list to a target concentration — completely independent of pooling. Enter each sample's stock concentration; every other parameter defaults to the shared values below but can be overridden per row. Serial steps appear automatically when one dilution can't reach the target within the well limit. C1V1 = C2V2; bench reference only, no robot file.

Unit

Default target conc*

Default final volume µL*

Default min transfer µL

Default max well/tube capacity µL

Default round to µL

#	Name	In well	Out well	Stock conc*	Target	Final µL	Min µL	Max µL	Round µL

Independent of the pool above. Any blank cell falls back to the matching shared default above.

About the numbers

Molarity for dsDNA: nM = conc(ng/µL) × 10⁶ / (660 × size_bp). Direct nM can be entered when molarity has already been measured. Transfers are calculated as equal fmol per sample, then rounded to the selected increment and audited for post-rounding deviation. Low transfer volumes can be handled by warning only, increasing final pool volume, or producing a pre-dilution plan. In fmol mode, the tool derives target nM as total fmol divided by final volume.

PoolMate - User Guide

Quick bench reference for choosing the correct workflow and understanding required fields.

Which tab do I use?

Pool — combine several libraries into one tube (or normalize each into its own well).

Normalize — dilute every library to one common concentration, plate → plate.

Dilute — dilute one sample or a list, as tubes on the bench or plate → plate.

Load — work out how much of your pool(s) to load onto an ONT or Illumina flow cell.

Each tab is self-contained: its own inputs, its own live graphic, its own export.

Pool — step by step

1. Enter each sample: source well, name, and either concentration + size bp or direct nM.

2. Set Target pool nM (or total fmol) and Total final volume.

3. Choose Layout: Tube pools everything into one tube; Plate puts each sample in its own well.

4. Click Generate worklists for DNA.csv + Buffer.csv.

The three Pool actions

Calculate molarities — quick nM check from the sample table only; no volumes.

Quick pool table — a manual pipetting table; no robot files. Choose the target style that suits you: fmol per sample, total fmol, target nM in a final volume (Illumina style), or an equal volume from every sample.

Generate worklists — the full epMotion export with deck, buffer, and tips.

Normalize — step by step

1. Pick the unit (nM or ng/µL), a target concentration, and a final volume per well.

2. Enter each library's input well and concentration.

3. Optionally set an Output well to move a library (e.g. A3 → D5); blank keeps the same well.

4. Download Normalization worklists for the plate-to-plate run.

Dilute — step by step

Enter each sample's stock concentration; target, volume, min transfer, max capacity and rounding all default to the shared values and can be overridden per row.

Switch between Tube view (bench) and Plate view (plate → plate). Set In well / Out well to control placement.

Download epMotion worklists runs the dilution on your pooling script as a separate run.

Load — step by step

1. Pick the platform and a flow cell / kit preset; the target load or loading concentration fills in and stays editable.

2. Choose One pool or Combine several pools, then enter each pool's concentration (nM, or ng/µL + size bp).

3. With several pools, Share sets the relative amount of each — all 1 gives equal molar representation.

4. Calculate loading gives the µL to take from each pool plus the bench steps.

Load — what you get

Oxford Nanopore: the µL of each pool, the Elution Buffer top-up to fill the library slot, and the loading mix (SB + Library Beads + library) to load via the SpotON port.

Illumina: the combined pool molarity, then the dilution steps down to the loading pM in the final volume — split into serial steps when a single step is not pipettable. The denature step is instrument-specific and is not calculated; follow your Denature and Dilute guide.

Presets are vendor starting points — always confirm against your kit and instrument SOP.

Choosing output wells

Anywhere a task writes to a plate, the Out well column decides where each sample lands. Leave it blank to keep the sample in its own well.

The live graphic shows the move, and the exported DNA/Buffer worklists follow it exactly.

Deck & racks

Rack 1 = source plate. Rack 2 = destination (a pool tube in Tube layout). Buffer is drawn from the reservoir at position "1" on the buffer rack, which normally matches the source rack.

Tools: TS_50 = 50 µL tips, TS_300 = 300 µL tips.

Too concentrated? (< 1 µL)

If a transfer would fall below the minimum, dilute first, then pool — a pooling script cannot dilute and pool in one run.

Either use Dilute → export worklists → run → mix, or set Low-volume handling to pre-dilute for a Dilution.csv plan.

Saving & output files

A plain reload always starts blank; use Save run (JSON) to keep work and Open run to restore it (a recovery banner offers unsaved work).

DNA.csv transfers sample, Buffer.csv transfers diluent, worksheet is the calculation record, inputs re-imports into PoolMate.