Nanopore sequencing data is stored in three file types: POD5, FASTQ and BAM.

Basecalling summary information is stored in a sequencing_summary.txt file:

POD5 is an Oxford Nanopore-developed file format which stores nanopore data in an accessible way and replaces the legacy .fast5 format. This output also reads and writes data faster, uses less compute and has smaller raw data file size than .fast5.

FASTQ is a text-based sequence storage format, containing both the sequence of DNA/RNA and its quality scores.

BAM files are output if you perform alignment or modified base calling on the basecalled dataset.

sequencing_summary.txt contains metadata about all basecalled reads from an individual run. Information includes read ID, sequence length, per-read q-score, duration etc. The size of a sequence summary file will depend on the number of reads sequenced.

Example file sizes below are based on different throughputs from an individual flow cell, with a run saving POD5, FASTQ, and BAM files with a read N50 of 23 kb. TMO = theoretical maximum output.

The storage capacity of the P24 or P48 Data Acquisition Units is approximately 24 hours of 24 or 48 flow cells, respectively, with .fast5 and FASTQ output.

The onboard storage on the PromethION tower is designed as temporary storage, when running the device at full capacity it is essential that this data is streamed from the device in real-time to prevent runs from terminating due to a lack of storage space. See here for guidance on transferring data.

The device should not be used for long term storage of sequencing data. Oxford Nanopore cannot be held responsible for loss of data stored on the device in the event of a drive failure.