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How do I transfer data off my PromethION?
How do I transfer data off my PromethION?
The storage capacity of the P24 or P48 Data Acquisition Units is insufficient for 72-hour runs on 24 or 48 flow cells with POD5 and FASTQ output enabled.
Therefore, it is essential that the data is streamed from the device in real-time to prevent runs from terminating due to lack of storage space. Please refer to the Remote transfer section of the MinKNOW manual and to the Data management section of the PromethION 24/48 user manual for more details. We recommend consulting your internal IT department to identify the most suitable solution.
The connectivity to the local infrastructure must be of sufficient bandwidth to prevent data build-up. The PromethION offers two 10-Gbit-per-second ports, with the ability to choose between Ethernet or Fibre solutions. USB ports do not provide sufficient bandwidth for real-time data transfer and should therefore not be used.
Below is a worked example showing idealised data transfer speeds; real transfer speeds could be slower depending on network configuration:
| 1 Gbit/s | 10 Gbit/s | |
|---|---|---|
| 1 x 200-Gbase flow cell | ~7 hrs | ~1 hr |
| 48 x 200-Gbase flow cell | ~320 hrs | ~32 hrs |
The PromethION runs Ubuntu and can mount multiple file system types. We recommend storage presented as NFS or CIFS. This storage should be SSD for its high write speed compared to HDD. After initial writing to networked SSD drives, data can be moved to storage with a slower write speed for long-term storage.
The form and volume of data to be stored will depend on user requirements:
Storing .pod5 files with raw read data is optional. It permits re-basecalling of data when required. Further, selected third-party tools use the raw signal information contained within the .pod5 to extract additional information from the raw signal, e.g. modified basecalling.
Retaining basecalled FASTQ and/or BAM files allows the use of standard downstream analysis tools.
Oxford Nanopore is unable to provide exact recommendations for storage, as these will be site-specific. The above guidelines and requirements should be taken into consideration.
