FASTQ is a type of file used to represent DNA sequences by nitrogenous bases, and their due quality scores. It is the result of converting the information generated by the sequencing technology used in data with biological information.
For example, Illumina uses image analysis, while Thermo Fisher uses the concentration of H+ released during a synthesis reaction.
The face of FASTQ
A FASTQ file has as its basic unit 4 main information:
(1) Contains string identifier information (usually, it is the read name). It starts with “@”
(2) Contains base sequence information
(3) The exclusive line beginning with “+” indicates the end of the base sequence and the start of quality information on the next line, acting as a information delimiter.
(4) Contains quality information for each base represented in (2). This quality is expressed in ASCII encoding, and It can change according to the version and/or technology used.
The pairs of reads have the same sequence identifier plus a numeric indicator related to the direction of read (forward or reverse). This numbering can be different according to the technology used and/or the conversion program used to obtain the FASTQ.
Author: Livia Moura, PhD.