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How to determine the encoding method of quality score in a fastq file?

As you know, there are two general standards for the sequencing quality of fastq files: Phred+33 and Phred+64.

I have a very old fastq file that was generated on Genome Analyzer IIx platform (FC-104-50xx). I am not sure about the score of this fastaq has it gone through some conversions, is there some simple way to infer from the fastq total whether his sequencing quality score is Phred+33, Solexa+64 or Phred+64

fastq samtools bwa ngs
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updated by Juke34 Juke34 • written by octpus616 • octpus616

Try seqkit convert which converts FASTQ quality encoding between Sanger, Solexa and Illumina.

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written by shenwei356 shenwei356

Since this file has been generated for a long time, I'm not quite sure if it has undergone some kind of conversion, is it possible to test the encoding way?

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written by octpus616 • octpus616

1 answer

You can use gaas_fastq_guessMyFormat.pl from GAAS

e.g. with conda

conda create -n gaas_env gaas
conda activate gaas
gaas_fastq_guessMyFormat.pl -i myfile.fastq.gz
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written by Juke34 Juke34

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