Version Compatibility

Reference examples tested with: BioPython 1.83+, numpy 1.26+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Long-Read Quality Control

"Check the quality of my Nanopore/PacBio run" → Generate read length distributions, quality score plots, and summary statistics, then filter reads by length and quality thresholds.

• CLI: NanoPlot --fastq reads.fq.gz -o nanoplot_output/, chopper -q 10 -l 1000 < reads.fq > filtered.fq

NanoPlot - Visualization

# From FASTQ
NanoPlot --fastq reads.fastq.gz -o nanoplot_output -t 4

# From BAM
NanoPlot --bam aligned.bam -o nanoplot_output -t 4

# From sequencing summary (fastest)
NanoPlot --summary sequencing_summary.txt -o nanoplot_output

NanoPlot - Common Options

NanoPlot --fastq reads.fastq.gz \
    -o nanoplot_output \
    -t 8 \
    --N50 \                        # Show N50 in plots
    --title "Sample QC" \
    --plots hex dot \              # Plot types
    --format png pdf \             # Output formats
    --color darkblue \
    --maxlength 50000 \            # Max length for plots
    --minlength 500                # Min length for plots

NanoStat - Statistics Only

# Quick statistics (no plots)
NanoStat --fastq reads.fastq.gz --threads 4

# From BAM
NanoStat --bam aligned.bam --threads 4

# Output to file
NanoStat --fastq reads.fastq.gz --threads 4 > qc_stats.txt

chopper - Filter Reads

# Filter by length and quality
gunzip -c reads.fastq.gz | chopper -q 10 -l 1000 | gzip > filtered.fastq.gz

# Quality >= 10, length >= 1000bp