FASTQ
formats
Unfortunately, the FASTQ format is not standardized. There are several variants
in common use, and it is not possible to distinguish them automatically with
high reliability. The main parameters are the minimum and maximum Q scores and
the ASCII_BASE constant.
The fastq_chars command can be
used to guess the format of a FASTQ file.
ASCII coding of Q scores
The Q value is coded as a printable
ASCII character using Q =
ASCII_CODE - ASCII_BASE. Here, ASCII_CODE is the ASCII code for the character
and ASCII_BASE is a constant. The original Sanger FASTQ format used ASCII_BASE =
33 so for example if the quality score is coded as 'C' then Q = ASCII_CODE('C')
- 33 = 67 - 32 = 35. See here for tables mapping
ASCII characters to Q scores for common variants of FASTQ.
| Option | Default | Description |
| -fastq_ascii | 33 | ASCII_BASE constant described above. |
| -fastq_qmin | 0 | Minimum Q score. |
| -fastq_qmax | 41 | Maximum Q score (input files). |
| -fastq_qmaxout | 41 | Maximum Q score (output files). |