In the fastq format every 4k+4-th line contains the positionwise qualityscore (ascii encoded):
@SEQ_ID
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
...
which program uses this information besides trimming tools (cutadapt) or quality control (fastqc)?
I heard that segemehl (mapping) abandons this quality string in favor of running time (maybe other mapping tools too?) But what about abyss, trinity, ...?
UPDATE:
So i atrifically generated a fastq file containing 2 identical reads that perfectly match a sequence in some genome (C.fna). The two reads have the most extreme phred scores (only '!!'=highest sanger phread and only 'II'=lowest sanger phred)
Now using segemehl the mapping quality is identical (60)
@HD VN:1.0
@SQ SN:C_fna LN:15440
@RG ID:A1 SM:sample1 LB:library1 PU:unit1 PL:illumina
@PG ID:segemehl VN:0.3.4 CL:segemehl -i C2.fna.idx -d C2.fna -q test.fq
A 0 C_fna 261 60 220= * 0 0 ACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! HI:i:0 NH:i:1 NM:i:0 MD:Z:220 RG:Z:A1 YZ:Z:0
B 0 C_fna 261 60 220= * 0 0 ACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII HI:i:0 NH:i:1 NM:i:0 MD:Z:220 RG:Z:A1 YZ:Z:0
[SEGEMEHL] Thu Feb 6 08:35:15 2020: matching w/ suffixarray has taken 0.000000 seconds.
So segemehl does NOT use the read quality phred (basically only using the read sequence for mapping)