bb_plot_quality_per_base - ampinzonv/BB3 GitHub Wiki
Function: bb_plot_quality_per_base
Plot an ASCII vertical histogram showing average quality per base position from a FASTQ file.
๐ Description
This function calculates the average quality score for each base position across a sample of FASTQ reads. The result is plotted as a vertical ASCII histogram showing quality scores by base position.
๐ฅ Input
- FASTQ file (plain or gzipped)
- STDIN is supported via
--input -
๐ค Output
- An ASCII chart showing vertical bars of quality scores per base position.
- Default output is STDOUT, or you can specify a file with
--outfile.
๐งช Examples
Use 10% of reads (default):
bb_plot_quality_per_base --input reads.fastq
Use 25% of reads and change Phred offset:
bb_plot_quality_per_base --input reads.fastq --sample_size 25 --phred_offset 64
Save plot to file:
bb_plot_quality_per_base --input reads.fastq --outfile qual_per_base.txt
Use compressed input:
bb_plot_quality_per_base --input reads.fastq.gz
โ๏ธ Usage
bb_plot_quality_per_base --input FILE [--sample_size PCT] [--phred_offset N] [--outfile FILE] [--quiet] [--force]
๐งต Options
| Option | Description |
|---|---|
--input FILE |
FASTQ file or - for STDIN (required) |
--sample_size PCT |
Percentage of reads to sample (default: 10) |
--phred_offset N |
ASCII offset for quality encoding (default: 33) |
--outfile FILE |
Output file for the histogram (default: STDOUT) |
--quiet |
Suppress log messages |
--force |
Overwrite output file if it exists |
๐ Notes
- ASCII histogram uses
*and|symbols to display the vertical plot. - Output includes X-axis position labels and Y-axis quality scale.
- Works well for detecting base-specific drops in read quality (e.g., 3'-end degradation).