bio-basecalling
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. Note: Guppy is deprecated; use Dorado for all new analyses.
npx skills add BioTender-max/awesome-bio-agent-skills --skill basecalling --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Nanopore Basecalling **"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 (Recommended) Dorado is ONT's current production basecaller, replacing Guppy. It offers better accuracy and speed. ### Basic Basecalling ```bash dorado basecaller sup pod5_dir/ > calls.bam ``` ### Choose Model ```bash dorado basecaller fast pod5_dir/ > calls.bam dorado basecaller hac pod5_dir/ > calls.bam dorado basecaller sup pod5_dir/ > calls.bam ``` ### Model Speed vs Accuracy | Model | Speed | Accuracy | Use Case |
- Version Compatibility
- Dorado (Recommended)
- Basic Basecalling
- Choose Model
- Model Speed vs Accuracy
- Specific Model Version
- List Available Models
- Output FASTQ Instead of BAM
- Modified Base Detection
- GPU Selection
- Batch Size for Memory
- Duplex Calling
- Demultiplexing During Basecalling
- Trim Adapters
dorado basecaller sup pod5_dir/ > calls.bam dorado basecaller fast pod5_dir/ > calls.bam dorado basecaller hac pod5_dir/ > calls.bam dorado download --model dna_r10.4.1_e8.2_400bps_sup@v5.1.0 dorado basecaller dna_r10.4.1_e8.2_400bps_sup@v5.1.0 pod5_dir/ > calls.bam dorado download --list dorado basecaller sup pod5_dir/ --emit-fastq > calls.fastq dorado basecaller sup,5mCG_5hmCG pod5_dir/ > calls_mods.bam dorado basecaller sup,5mCG pod5_dir/ > calls_5mc.bam dorado basecaller sup,6mA pod5_dir/ > calls_6ma.bam
What does the bio-basecalling skill do?
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. Note: Guppy is deprecated; use Dorado for all new analyses.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill basecalling --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.