bb_plot_quality_distribution - ampinzonv/BB3 GitHub Wiki

Function: bb_plot_quality_distribution

Plot ASCII histogram of average quality per read from a FASTQ file.

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🔍 Description

This function computes the average quality score per read and groups them into bins (e.g. 0–9, 10–19, etc.). The distribution is displayed as an ASCII histogram.

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📥 Input

• A FASTQ file or --input - to use STDIN.
• Gzip-compressed .fastq.gz files are supported.

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📤 Output

• Histogram showing how many reads fall into each average quality range.

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🧪 Examples

Use default sampling:

bb_plot_quality_distribution --input reads.fastq

Sample 30% and save plot:

bb_plot_quality_distribution --input reads.fastq --sample_size 30 --outfile plot.txt

Specify Phred offset:

bb_plot_quality_distribution --input reads.fastq --phred_offset 64

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⚙️ Usage

bb_plot_quality_distribution --input FILE [--sample_size PCT] [--phred_offset N] [--outfile FILE] [--quiet] [--force]

🧵 Options

Option	Description
--input FILE	FASTQ file or - for STDIN (required)
--sample_size PCT	Percentage of reads to sample randomly (optional)
--phred_offset N	ASCII offset for quality encoding (default: 33)
--outfile FILE	Output file (default: STDOUT)
--quiet	Suppress informational messages
--force	Overwrite output file if it exists

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📌 Notes

• Output bins include ranges: 0–9, 10–19, 20–29, ... up to 60–69.
• A quick way to inspect general sequencing quality across reads.