Four lines define each entry in a FASTQ file
@AY01234 # sequence-ID (and description)
GCATCTCGA... # FASTA-like (nucleotide) sequence
+ # quality header line (optional: repeated sequence-ID, usually empty)
BF7'F<0&F... # →Quality values of each sequence position
FASTQ example
Three entries of forward read sequences (Illumina R1 FASTQ file):
@A0216:173:HJNFKDSX:3:1101:2745:1016 1:N:0:TTACGCAC+AGATGGTC
GGGAGACGAGCGTCACGTTCATGAGCGCCTCCTCGACCTCGTCGACGGAGTCGAAATTACGCGCCACCCACAGCGGAAATTCGAACGTGGCGACGTTTTCC
+
BBBFBFFFFFFFBF<FBB0B<BF<FFFFFIIII'<<FF7BF<'7<BBBBB<<BBBBBBBBBBBBBBBBBBBBBB<7BB<<B<BFB<BBBB77<BB<BBBBB
@A0216:173:HJNFKDSX:3:1101:3884:1016 1:N:0:TTACGCAC+AGATGGTC
GCTTCGCCTTGCCGCCCGCACCAAACACCGTGTCATAGTGGTAGCCGCGCGGAGTAACCAAGATGGTCTCCCCATATGAGAAACTCCAGTCGAGATTACGG
+
BBBFFFFFFFFFFFFFIBFFIIIFFIIBBF0BFFF0BF<BF<BBFFBFFB<BBFBBBF0<BBFFFBBBFBBFFFBBBF<<BBBBFFFFB<BBFFFBBBB07
@A0216:173:HJNFKDSX:3:1101:4010:1016 1:N:0:TTACGCAC+AGATGGTC
TATTTTTATGCATTTGCTTAATTTTAATAGCTGCAAAAGTTAATAAAATAAAACCAATTGCTACAAAAAAAGAAGTGCAGCTTCAAGAAGATGTAAAACTG
+
<<<<<0<00000<BB7BBBB000BB0<7BB000B<0BB'<<<'0'0'<0<00'07BB'77''07<7''0000'7<<0'0<<''7<'7'77'000'77'''7
Meaning of Illumina sequence names
@instrumentID:run:lane:tile:xPos:yPos direction(R1 or R2):quality(N=ok filtered):index sequence pairs
→ Paired-end reads explained by Torsten Seemann
→ awk: How to add "/1" and "/2" to FASTQ sequence-IDs