MinKNOW¶
MinKNOW supports outputting reads as either raw or basecalled data. The following sections describe the different formats and how to use them.
Raw output formats¶
| Format | Supported | Default | Generation time |
|---|---|---|---|
| POD5 | ✓ | ✓ | As batch is filled, during acquisition and basecalling catchup |
| .fast5 | ✓ Deprecated |
✗ | As batch is filled, during acquisition and basecalling catchup |
Basecalled output formats¶
| Format | Supported | Default | Generation time |
|---|---|---|---|
| BAM | ✓ | ✗ | As batch is filled, during acquisition and basecalling catchup |
| FASTQ | ✓ | ✓ | As batch is filled, during acquisition and basecalling catchup |
Other data formats¶
These formats are output by MinKNOW by default, and are not configurable.
| Format | Generation time |
|---|---|
| Sequencing Summary | End of sequencing acquisition and basecalling catchup period. |
| Sample Sheet | Beginning of sequencing run. |
| Final Summary | Once all files have been written for the sequencing run. |
| Barcode Alignment Report | End of sequencing acquisition and basecalling catchup period. |