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README clarification
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@dialvarezs
dialvarezs committed Aug 26, 2024
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Expand Up @@ -38,7 +38,7 @@ Uses Dorado for basecalling and demultiplexing.
| `output_dir` | No | `demultiplex_results` | Directory for saving results. |
| `fastq_output` | No | `true` | Generates FASTQ files if `true`; otherwise, generates UBAM files. |
| `qscore_filter` | No | `10` | Minimum QScore threshold for "pass" data, used in demultiplexing. |
| `dorado_basecalling_model` | No | `sup` | Model used for basecalling. |
| `dorado_basecalling_model` | No | `sup` | Model used for basecalling. Check Dorado help for available options. |
| `dorado_basecalling_extra_config` | No | - | Additional configuration options for Dorado basecalling. |
| `dorado_basecalling_gpus` | No | `1` | Number of GPUs to allocate for basecalling. |
| `skip_demultiplexing` | No | `false` | Skips demultiplexing if `true`. |
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