escpod filter¶

Extract specific reads from a POD5 file based on read IDs.

Usage¶

escpod filter -i <IDS_FILE> -o <OUTPUT> <INPUT>

Arguments¶

Options¶

ID File Format¶

The IDs file should contain one UUID per line:

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

Supported Formats¶

• Standard UUID: a1b2c3d4-e5f6-7890-abcd-ef1234567890
• No dashes: a1b2c3d4e5f67890abcdef1234567890
• Comments (lines starting with #) are ignored
• Empty lines are ignored

Examples¶

Basic Filtering¶

Create a file with read IDs:

cat > interesting_reads.txt << EOF
a1b2c3d4-e5f6-7890-abcd-ef1234567890
b2c3d4e5-f6a7-8901-bcde-f12345678901
EOF

Filter the POD5 file:

escpod filter -i interesting_reads.txt -o filtered.pod5 experiment.pod5

Filter from Basecalling Results¶

If you have basecalling results with read IDs of interest:

# Extract read IDs from a BAM file (requires samtools)
samtools view aligned.bam | cut -f1 | sort -u > mapped_reads.txt

# Filter POD5 to only mapped reads
escpod filter -i mapped_reads.txt -o mapped.pod5 experiment.pod5

Filter Using Another POD5 File¶

Extract reads that exist in another file:

escpod inspect reads reference.pod5 > reference_ids.txt
escpod filter -i reference_ids.txt -o matching.pod5 experiment.pod5

Output¶

The command prints filtering statistics:

Filtering experiment.pod5 using IDs from interesting_reads.txt
Output: filtered.pod5
Loaded 100 read IDs to filter
Filtered 95 reads from 10000 total (0.95%)
Warning: 5 requested IDs were not found in the input file

Notes¶

• Only reads with matching IDs are included in output
• Run info is preserved for all matching reads
• Signal data is re-compressed in the output
• A warning is shown if some requested IDs are not found