FASTQ sequence format

From BioPerl

Description

A file format used frequently at the Wellcome Trust Sanger Institute to bundle a FASTA sequence and its quality data.

Fastq files have sequence and quality data on a single line and the quality values are single-byte encoded. To retrieve the decimal values for qualities you need to subtract 33 (or Octal 41) from each byte and then convert to a '2 digit + 1 space' integer.

The original FASTQ file format can be parsed by the Bio::SeqIO system using the Bio::SeqIO::fastq module. However, Illumina FASTQ doesn't parse correctly yet.

See also:

• the Qual format.
• Sanger FASTQ format and the Solexa/Illumina variants
• FASTQ on Wikipedia
• MAQ page on FASTQ format

Example

@NCYC361-11a03.q1k bases 1 to 1576
GCGTGCCCGAAAAAATGCTTTTGGAGCCGCGCGTGAAAT...
+NCYC361-11a03.q1k bases 1 to 1576
!)))))****(((***%%((((*(((+,**(((+**+,-...

See also

• Bio::Seq::Quality
• An example of creating FASTQ from FASTA and QUAL has been scrapbooked here.