What is a FASTQ file?

A text file that contain the sequence information and quality scores per read

Written by Rani Powers, PhD

A FASTQ file contains four details for each read in the following format:

  1. Sequence identifier and/or a description

  2. Sequence letters

  3. + and/or repeat of line 1 details

  4. Encoding of line 2 with the same amount of letters/characters

Line 4 provides the quality of the sequence in line 2 using a 21 character code, where each symbol stands for a certain level of quality. The code is provided below, with the “!” representing the lowest quality and “~” representing the highest.


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