GenomicsForOneHealth

Compact Nanopore Guide

This page supports the selector without turning every wizard step into a lecture. Use it when you want the reasoning behind kit, flow cell, basecalling, or analysis-environment recommendations.

Back to the advisor

Input material

Start with the material, not the kit

The selector splits route choice from Nanopore setup because the first real decision is what kind of material the data represent: long-read metagenomic DNA, RNA virome material, 12S amplicons, single isolates, barcoded isolates, or clinical metagenomes.

High-molecular-weight DNA

Best fit for isolate assembly, plasmid resolution, and longer-fragment metagenomics where read length and consensus quality matter.

Amplicons and targeted products

These behave differently from shotgun DNA. They usually need lighter throughput assumptions and primer-aware cleanup rather than metagenomic assembly defaults.

Environmental or clinical metagenomes

Mixed-community inputs need more caution around host background, community complexity, and whether a cloud or ONT-curated fallback may be more appropriate than a study-specific repo backend.

RNA and cDNA

Native direct RNA and cDNA-derived RNA workflows should not be collapsed into generic DNA logic. They can change flow cell, throughput, and basecalling expectations.

What this changes in the selector

The first routing pages ask for sample, material, and target before any Nanopore setup questions appear.

Flow cells

Choose throughput and compatibility deliberately

MinION R10.4.1

The clean default for most new microbial genomics and moderate-depth metagenomics runs.

PromethION R10.4.1

Deep metagenomics, larger cohorts, or cases where a MinION-style throughput assumption is too small.

RNA-specific flow cells

Relevant only for native direct RNA. They should not be shown for ordinary DNA workflows.

What this changes in the selector

Flow cell choice is a separate setup page because it changes throughput framing and compatibility notes, not the biological route itself.

Library prep kits

Kit choice changes preprocessing more than route identity

LSK114

Strong default for read length, yield, and consensus-focused workflows. Best when single-sample quality matters more than speed.

RBK114.24

Rapid multiplexing. Expect demultiplexing and barcode trimming before downstream analysis.

NBD114.24

Native barcoding with stronger quality framing than rapid barcoding, while still preserving per-barcode separation logic.

Amplicon and RNA-specialized routes

Amplicon workflows and direct RNA should be treated as distinct setup branches, not squeezed into generic DNA assumptions.

What this changes in the selector

The setup advisor shows four kit consequences only: demultiplexing, barcode trimming, typical use, and route implication. That keeps the page readable while still exposing the operational impact.

Basecalling tiers

FAST, HAC, and SUP are different intent choices

FAST

Best for live monitoring, quick triage, or field-style early decisions.

HAC

The standard balanced default for most production microbial genomics and metagenomics workflows.

SUP

Prefer this when assembly quality, AMR interpretation, or high-confidence consensus matters most.

Already basecalled

Use this when FASTQ or BAM already exists so the selector stops inserting upstream basecalling advice.

What this changes in the selector

Basecalling becomes a clean setup page. It no longer clutters route choice, but it still changes early-step guidance and whether the result inserts a basecalling action at all.

EPI2ME Labs

Use EPI2ME Labs when you need an ONT-curated general workflow shell

EPI2ME Labs is useful when the nearest internal example is informative but still too study-specific. It fits especially well for bacterial genomes, metagenomics, and ONT amplicon-style reference workflows.

  • Good fit for isolate assembly and polishing.
  • Good fit for generalized long-read metagenomics when the repo only has an approximate example.
  • Useful as an amplicon reference, but not an exact replacement for every 12S study design.

What this changes in the selector

Supported routes may show EPI2ME Labs as an alternative environment. Unsupported routes surface it more strongly as a fallback.

CZ ID

Use CZ ID when the main value is cloud metagenomic interpretation

CZ ID is most relevant for long-read metagenomics, clinical metagenomes, and some unsupported environmental discovery contexts where a cloud analysis environment is more practical than forcing everything into a study-specific internal backend.

  • Best aligned to metagenomic interpretation, not isolate assembly.
  • Useful when the repo only offers a nearest example rather than an exact route.
  • Less suitable for small isolate assembly or narrowly targeted amplicon questions.

What this changes in the selector

CZ ID appears only on metagenomic-style setup pages and is prioritized mainly for unsupported or hybrid-reference outcomes.

Practical defaults

Simple defaults for common microbial genomics and metagenomics cases

Environmental long-read DNA

Default to R10.4.1 plus HAC for broad profiling, or SUP when assembly and AMR matter more.

Single isolates

Default to LSK114 plus SUP. Keep hybrid assembly visible when short reads also exist.

Barcoded isolates

Default to native barcoding plus SUP. Keep per-barcode separation and comparative outputs explicit.

Metagenomic short-read-like long reads

If the median read length drops below 1000 bp, the selector shifts the preferred assembly heuristic toward nanoMDBG.

What this changes in the selector

The conditions page stays small. It only asks for a few route-specific refinements that actually change tool preference, warnings, or early-step emphasis.

Matrix snapshots

Recent literature by sample type

These sections stay short on purpose. They are matrix-specific notes that the selector can point to when a route is supported, approximate, or still guide-only.

Loading matrix-specific guide sections...