Sequencing software MinKNOW

for NGS sequencingfor genomicsdata management

Overview
MinKNOW is the control and acquisition software for Oxford Nanopore devices. It manages device connection and control, data acquisition, live and post-run basecalling, real-time analysis, flow cell and hardware checks, run configuration and reporting. Document identifier: MKE_1013_v1_revDN_29Apr2026.

Supported devices and scope

• MinION Mk1B, MinION Mk1D
• MinION Mk1C
• Flongle adapter and Flongle Flow Cells
• GridION
• PromethION 24 / 48
• PromethION 2 Solo (P2 Solo) and PromethION P2i

Key capabilities

• Device control and connection manager for local or remote access
• Hardware checks via Configuration Test Cell (CTC) and flow cell active pore assessment
• Start, pause, stop and monitor sequencing experiments
• Live basecalling (Fast / HAC / SUP) and optional post-run basecalling
• Barcoding (single/dual), barcode trimming and assignment
• Alignment during runs using FASTA/.mmi references and optional BED intervals
• Adaptive sampling (enrich/deplete) with barcode-balancing workflows
• Data output: FASTQ (gzip), BAM, POD5 with configurable splitting and compression
• Run templates, sample-sheet (CSV) upload and multi-flow-cell experiment support
• Run targets and stopping rules (time, estimated/basecalled bases, coverage)
• Exportable run reports and pore-activity CSVs

Quick start guides and major sections

• Device-specific quick starts (MinION, GridION, PromethION, Flongle)
• Computer requirements and installation on Windows, macOS, Linux
• Updating procedures and Connection Manager workflow
• Homepage, Sequencing overview, hardware and flow cell checks
• Starting and monitoring runs, pausing and recovering experiments
• Post-run analysis: basecalling, barcoding, alignment and reporting

Output and file format highlights

• Basecalled formats: FASTQ (gzip optional) and BAM (Crypt4GH support)
• Raw signal: POD5 recommended (legacy FAST5 support deprecated)
• Basecaller models: Fast, HAC (default), SUP (highest accuracy)
• Advanced controls: reads-per-file, time-based splitting, barcode-based splitting and compression

Computer and installation notes

• Distribution: zip for Windows, package for macOS, apt repository/package for Ubuntu Linux
• Data storage recommended on SSD; output location configurable
• Proxy and advanced network settings configurable via user_conf

Tutorials, help and troubleshooting

• In-app tutorials on first launch (resettable)
• Help menu: support links, logs export (TGZ) and troubleshooting guides
• OS-specific log locations and export procedures

Security and device settings

• Device security: firewall defaults, remote access controls, SSH enable/disable
• Recommendation: restrict remote access on untrusted networks and follow local data protection policies

Characteristics / technical specifications

• Product type: Sequencing control and acquisition software
• Manufacturer / brand: Oxford Nanopore Technologies
• Document version: MKE_1013_v1_revDN_29Apr2026
• Supported devices: MinION Mk1B/Mk1D/Mk1C, GridION, PromethION 24/48, PromethION 2 Solo, Flongle
• Basecalling engines: Dorado server / Fast, HAC, SUP
• Raw formats: POD5 (default when enabled); FAST5 deprecated
• Basecalled outputs: FASTQ (gzip) and BAM
• Adaptive sampling: enrich/deplete with optional on-target basecalling
• Sample sheet: CSV support for multi-flow-cell experiments
• Run termination rules: time, estimated/basecalled bases, coverage, barcode coverage, read counts
• Install platforms: Windows, macOS, Linux (Ubuntu 20/22/24)