SLOW5/BLOW5 are formats for storing raw Oxford Nanopore signal data with a focus on efficient parallel access and scalable analysis.

Note: SLOW5/BLOW5 are third-party community formats and are not officially supported by Oxford Nanopore Technologies (ONT).

TL;DR

  • SLOW5 is a human-readable text format for nanopore raw signal data.
  • BLOW5 is the binary compressed form of SLOW5, optimized for performance and storage.
  • Both formats are designed to improve I/O efficiency compared with legacy FAST5 workflows.
  • Typical records include read identifiers, run metadata, and raw signal vectors.
  • slow5tools is the core toolkit for inspect, conversion, merge/split, and indexing operations.

Structure

SLOW5 records are tab-delimited text with:

  1. Header/meta lines (global run metadata and field definitions)
  2. One line per read record
  3. Core per-read fields (for example read ID, digitisation/range/offset, sampling rate)
  4. Raw signal values

BLOW5 stores the same logical content in binary compressed form.

In practice:

  • Use SLOW5 when readability/interchange in text form is useful.
  • Use BLOW5 for large-scale processing, lower disk footprint, and faster random access.

Practical Conventions

  • Prefer BLOW5 for production workflows and large datasets.
  • Keep tool/version metadata with files for reproducibility.
  • Preserve read-group/run identifiers when converting between formats.
  • Index BLOW5 files when supported/needed by downstream tooling.
  • Use official converters (slow5tools) instead of custom parsers for transformations.

Common Pitfalls

  • Confusing text SLOW5 and binary BLOW5 in downstream command usage.
  • Losing metadata consistency when merging runs from different experiments.
  • Ignoring version compatibility between tools and file schema.
  • Treating signal-level files as sequence-level outputs.
  • Skipping integrity checks after large file transfers.

Common Uses

  • Raw nanopore signal storage
  • High-throughput signal processing workflows
  • Conversion pipelines between nanopore raw-data formats

Useful SLOW5/BLOW5 Tools

slow5tools view

Inspect SLOW5/BLOW5 content.

slow5tools view reads.blow5 | head

slow5tools stats

Generate quick file/read summary statistics.

slow5tools stats reads.blow5

slow5tools merge

Merge multiple SLOW5/BLOW5 files.

slow5tools merge run1.blow5 run2.blow5 -o merged.blow5

slow5tools split

Split a large file into smaller chunks.

slow5tools split reads.blow5 -d split_out/

slow5tools index

Create an index for random access.

slow5tools index reads.blow5