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bio-basecalling

Maintainer FreedomIntelligence · Last updated April 1, 2026

Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Guppy is deprecated; use Dorado for all new analyses.

OpenClawNanoClawAnalysisReproductionbio-basecalling🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcconvert

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-basecalling

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • CLI: dorado basecaller sup pod5/ > calls.bam (recommended), dorado basecaller sup,5mCG_5hmCG pod5/ (with modifications).
  • Basecall my Nanopore data" → Convert raw electrical signal (FAST5/POD5) into nucleotide sequences with quality scores, optionally detecting modified bases. CLI: dorado basecaller sup pod5/ > calls.bam (recommended), dorado basecaller sup,5mCG_5hmCG pod5/ (with modifications).
  • Convert raw electrical signal from Nanopore sequencing into nucleotide sequences.
  • Dorado is ONT's current production basecaller, replacing Guppy. It offers better accuracy and speed.

Source Doc

Excerpt From SKILL.md

Model Speed vs Accuracy

ModelSpeedAccuracyUse Case
fastFastestLowerQuick preview
hacMediumHighGeneral use
supSlowestHighestPublication quality

Guppy (Deprecated - Legacy Only)

Guppy is deprecated and no longer receiving updates. Use Dorado for all new analyses. Guppy examples below are only for maintaining legacy pipelines.

POD5 File Handling

POD5 is the new format replacing FAST5.

Use cases

  • Use when processing raw Nanopore data before alignment.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • long-read-alignment - Align basecalled reads
  • long-read-qc - QC after basecalling
  • medaka-polishing - Polish using basecalled reads
  • structural-variants - SV detection from long reads

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