FASTQ is a plaintext format for storing biological sequences and associated quality scores. It is similar to the FASTA format but in addition to sequence data it includes a quality score for each sequence element.

The commands Import and Export support this format.

Import produces an n×3 Matrix. Each row corresponds with a sequence element in the file:

the first column contains a sequence descriptor

the second column contains the sequence itself

the third column contains quality information

The FASTQ format employs the following standard IUB/IUPAC conventions for encoding protein or nucleic acid sequences as alphabetic characters. For details on this encoding, consult the FASTA format.

The quality string assigns a quality score to each element of the sequence. Each score is encoded as a single ASCII character with a mapping defined by the FASTQ specification.

Content-Type: chemical/seq-na-fastq

$\mathrm{Import}\left(''example/sample.fastq''\,\mathrm{base}=\mathrm{datadir}\right)$

Cock PJA, Fields CJ, Goto N, Heuer M, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research (2010) 38(6): 1767-1771, doi:10.1093/nar/gkp1137.