escpod view¶

Display reads from a POD5 file as a formatted table.

escpod view

Usage¶

escpod view [OPTIONS] <INPUT>

Arguments¶

Argument	Description
`<INPUT>`	Path to the POD5 file

Options¶

Option	Description
`--include <FIELDS>`	Comma-separated fields to include; names that aren't built-in read fields are read from the `.p5s` sidecar as annotation columns
`--exclude <FIELDS>`	Comma-separated list of fields to exclude
`--ids`	Only show read IDs
`--separator <SEP>`	Field separator (default: tab)
`--no-header`	Suppress header row output
`-o, --output <FILE>`	Write output to file instead of stdout
`-h, --help`	Print help

Output Fields¶

The default output includes:

Field	Description
`read_id`	Unique identifier (UUID)
`channel`	Channel number
`well`	Well number (1-4)
`read_number`	Sequential read number
`start_sample`	Start sample position
`num_samples`	Total signal samples
`end_reason`	Why the read ended

median_before (and pore_type, num_minknow_events, calibration_offset, calibration_scale, run_info, open_pore_level, expected_open_pore_level, selected_read_level, end_reason_forced) are available but not shown by default — pull them in with --include.

Examples¶

Basic Usage¶

escpod view experiment.pod5

Output:

read_id                               channel  well  read_number  num_samples
a1b2c3d4-e5f6-7890-abcd-ef1234567890  1        1     1            50000
b2c3d4e5-f6a7-8901-bcde-f12345678901  1        1     2            75000
c3d4e5f6-a7b8-9012-cdef-123456789012  2        1     1            62000
...

Show Only Read IDs¶

escpod view --ids experiment.pod5

Output:

a1b2c3d4-e5f6-7890-abcd-ef1234567890
b2c3d4e5-f6a7-8901-bcde-f12345678901
c3d4e5f6-a7b8-9012-cdef-123456789012

Save to File¶

escpod view experiment.pod5 -o reads.tsv

Select Specific Fields¶

escpod view --include read_id,channel,num_samples experiment.pod5

Join Sidecar Annotations¶

Names that aren't built-in fields resolve as sidecar annotation columns (demux barcodes, design-derived conditions) and are appended after the built-in columns — unassigned reads get an empty cell:

escpod view reads.pod5 --include read_id,num_samples,barcode,condition

A name that matches neither a built-in field nor an annotation is a hard error listing what's available. Naming only annotations still emits the default built-in columns so rows stay keyed by read_id.

CSV Output¶

# Use comma separator for CSV format
escpod view --separator ',' experiment.pod5 -o reads.csv

# Without header for piping
escpod view --ids --no-header experiment.pod5 | head -n 10