CLI Reference¶
The escpod command-line tool provides utilities for working with POD5 files.
Usage¶
escpod <COMMAND> [OPTIONS]
Commands¶
These commands are in the default build — no extra Cargo features required.
| Command | Description |
|---|---|
| summary | Comprehensive file summary with QC metrics |
| view | Display reads as a table |
| inspect | Inspect file metadata and contents |
| merge | Combine multiple POD5 files |
| filter | Extract reads by ID list |
| bam-filter | Filter reads based on paired BAM file |
| subset | Split reads into multiple files based on CSV mapping |
Additional commands (repack, resquiggle, demux, index) live behind
Cargo feature gates — see the Experimental
section.
Global Options¶
-h, --help Print help information
-V, --version Print version information
Examples¶
Basic Workflow¶
# 1. Inspect what's in your files
escpod inspect summary run1.pod5
escpod inspect summary run2.pod5
# 2. View the reads
escpod view run1.pod5
# 3. Merge files from a run
escpod merge -o combined.pod5 run1.pod5 run2.pod5
# 4. Extract interesting reads
escpod filter -i selected_reads.txt -o subset.pod5 combined.pod5
Working with Multiple Files¶
Process all POD5 files in a directory:
# List all files
ls *.pod5
# Merge all files
escpod merge -o all_data.pod5 *.pod5
Extracting Read IDs¶
To get a list of read IDs from a file:
escpod inspect reads experiment.pod5 > read_ids.txt
Then filter another file:
escpod filter -i read_ids.txt -o filtered.pod5 other_experiment.pod5