wf-basecalling documentation

By EPI2ME Labs
1 min read

Basecalling workflow

This repository contains a nextflow workflow for basecalling a directory of pod5 or fast5 signal data with dorado and aligning it with minimap2 to produce a sorted, indexed CRAM.


This workflow introduces users to Dorado, which is now our standard basecaller. dorado is still under active development and will be kept updated as new releases are made. We strongly encourage users to check the CHANGELOG for breaking changes.


The workflow uses nextflow to manage compute and software resources, as such nextflow will need to be installed before attempting to run the workflow.

The workflow can currently be run using either Docker or Singularity to provide isolation of the required software. Both methods are automated out-of-the-box provided either Docker or Singularity is installed.

It is not required to clone or download the git repository in order to run the workflow. For more information on running EPI2ME Labs workflows visit out website.

Workflow options

To obtain the workflow, having installed nextflow, users can run:

nextflow run epi2me-labs/wf-basecalling --help

to see the options and running examples for the workflow.

Example command

nextflow run epi2me-labs/wf-basecalling \
    -profile singularity
    --input /path/to/my/fast5 \
    --dorado_ext fast5 \
    --ref /path/to/my/ref.fa \
    --out_dir /path/to/my/outputs \
    --basecaller_cfg "dna_r10.4.1_e8.2_400bps_hac@v3.5.2" \
    --basecaller_basemod_threads 2 \
    --remora_cfg "dna_r10.4.1_e8.2_400bps_hac@v3.5.2_5mCG@v2"

Choosing a model

The dorado repository has a table of available models to choose for --basecaller_cfg and --remora_cfg.

Updating the workflow

It is recommended to keep this workflow updated to take advantage of the latest basecalling models with:

nextflow pull epi2me-labs/wf-basecalling

Workflow outputs

The primary outputs of the workflow include:

  • two sorted, indexed CRAMs of basecalls, aligned to the provided reference, with reads separated by their quality score
    • <sample_name>.pass.cram contains reads with qscore >= threshold
    • <sample_name>.fail.cram contains reads with qscore < threshold

Take care to retain the input reference as CRAM files cannot be read without the corresponding reference!



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