escpod merge¶

Merge multiple POD5 files into a single output file.

escpod merge

Usage¶

escpod merge -o <OUTPUT> <INPUT>...

Arguments¶

Argument	Description
`<INPUT>...`	One or more POD5 files to merge

Options¶

Option	Description
`-o, --output <FILE>`	Output file path (required)
`-t, --threads <N>`	Number of threads for parallel processing
`--profile`	Enable profiling output with timing and throughput
`-h, --help`	Print help

Description¶

The merge command combines multiple POD5 files into a single file. This is useful for:

Combining files from different sequencing runs
Consolidating files split across multiple output files
Creating a single file for downstream analysis

Behavior¶

All reads from input files are copied to the output
Run info entries are deduplicated by acquisition ID
Signal data is re-compressed in the output file
The output file uses default compression settings

Examples¶

Merge Two Files¶

escpod merge -o combined.pod5 run1.pod5 run2.pod5

Merge All Files in Directory¶

escpod merge -o all_data.pod5 *.pod5

Merge with Explicit File List¶

escpod merge -o output.pod5 \
    /data/run1/file1.pod5 \
    /data/run1/file2.pod5 \
    /data/run2/file1.pod5

Output¶

The command prints progress information:

Merging 3 files into combined.pod5
  Processing: run1.pod5
    Added 5000 reads
  Processing: run2.pod5
    Added 4500 reads
  Processing: run3.pod5
    Added 5200 reads
Successfully merged 14700 reads into combined.pod5

Notes¶

Large files may take significant time to merge
Ensure sufficient disk space for the output file
The output file will be approximately the sum of input file sizes