POD5 Outputs¶
POD5 is Oxford Nanopore Technologies raw read format, based on Apache Arrow. Its specification is part of the repository which implements the format. You can also find documentation for the format here.
Specification¶
The POD5 file format is documented here.
Paths¶
The following path patterns are used to place the data on disk.
| File Path | Path pattern |
|---|---|
| POD5 Default | pod5{basecall_status_skip_or_empty}/{flow_cell_id}{basecall_status_skip_or_empty}_{short_protocol_run_id}_{short_run_id}_{batch_number}.pod5 |
| Split by barcode Enabled | pod5{basecall_status}/{alias}/{flow_cell_id}{basecall_status}_{alias_}{short_protocol_run_id}_{short_run_id}_{batch_number}.pod5 |
Note the pattern used is different when the option to split files by barcode is enabled.
See the Patterns documentation for more information on file patterns.
Read batching¶
The following batching options are used by default:
| Option | Value |
|---|---|
| Duration | 3600s |
| Bases | 500000000 Bases |
For more information on batching see Batching.
Minimum version¶
The minimum version POD5 files are expected to be written is 0.3.31.