sc_seqQual.py¶
Generate a heatmap from a FASTQ file to visualize sequencing quality across read positions.
Usage¶
Options¶
| Option | Description | Default |
|---|---|---|
-i, --infile | Input file in FASTQ format | Required |
-o, --outfile | Prefix of output files | Required |
-n, --nseq-limit | Maximum number of sequences to process | All |
--cell-width | Cell width (points) in heatmap | 12 |
--cell-height | Cell height (points) in heatmap | 10 |
--font-size | Font size (points) | 6 |
--angle | Column label angle (0, 45, 90, 270, 315) | 45 |
--text-color | Color of cell numbers | black |
--file-type | Output format: pdf, png, tiff, bmp, jpeg | |
--no-num | Omit numerical values from cells | Off |
--verbose | Print detailed debugging information | Off |
Output¶
Quality heatmap showing Phred scores per read position.