FASTQ sequence format

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Contents

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. FOr the standard Sanger version of FASTQ, 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. The most recent version (BioPerl v. 1.6.1) can parse variations of FASTQ [1] from Solexa and Illumina and interconvert them if the proper variants are designated (either 'sanger', 'illumina', or 'solexa').

See also:

Example

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

See also

References

  1. Cock PJ, Fields CJ, Goto N, Heuer ML, and Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2010 Apr;38(6):1767-71. DOI:10.1093/nar/gkp1137 | PubMed ID:20015970 | HubMed [fastq_paper]
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