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FASTQ format parameters

See also
FASTQ files
  FASTQ commands
Quality scores
  Wikipedia article on FASTQ
  Cock et ail (2010) paper describing FASTQ

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).