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| data:ont [2024/04/11 10:52] – Created the first draft Richard Bowers | data:ont [2024/06/10 11:03] (current) – Richard Bowers | ||
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| ==== Pod5 Files ==== | ==== Pod5 Files ==== | ||
| - | Pod5 is a proprietary format developed by Oxford Nanopore. It can be considered an intermediate format, but can also be reprocessed in a way that the Illumina intermediate files cannot. Thus we always deliver the Pod5 equivalent of the BAM or FASTQ from a sequencing run. | + | Pod5 is a proprietary format developed by Oxford Nanopore. It can be considered an intermediate format, but can also be reprocessed in a way that the Illumina intermediate files cannot. Thus we always deliver the Pod5 files as produced by the sequencer with the BAM or FASTQ data. |
| ===== File Naming ===== | ===== File Naming ===== | ||
| - | The files will be named using the same pattern as files from [[data: | + | The ONT data files have an additional component to them, here referred to as ''< |
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| + | In all other respects, the files will be named using the same pattern as files from [[data: | ||
| < | < | ||
| - | < | + | < |
| - | < | + | < |
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| </ | </ | ||
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| - | <SLX>.NoIndex.< | + | </code> |
| - | <SLX>.NoIndex.< | + | |
| + | The Pod5 files are delivered in a TAR file. The structure inside this file is the directory structure of the run's //pod5// directory. | ||
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| + | <SLX>.< | ||
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| The Pod5 files are large: typically nine times the size of the equivalent BAM. It is not practical to keep these files in the archive just in case they might be needed later. | The Pod5 files are large: typically nine times the size of the equivalent BAM. It is not practical to keep these files in the archive just in case they might be needed later. | ||
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| + | ===== Supporting Tools ===== | ||
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| + | Oxford Nanopore have produced a library for reading and processing Pod5 files. The documentation for this library is [[https:// | ||
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| + | The library comes with some Python tools around the C++ core that allow you to manipulate the files. There is one shortcoming in the tool set though: the ability to easily split a large Pod5 file into chunks of a fixed size (by number of reads). We have created a tool for this job, which is available at [[https:// | ||