Differences between setk and Biopython fastq-solexa conversion

[gittaylor]

Hi Heng,

I am using this toolkit to convert solexa (Illumina <1.3) to the newer format. I compared the output to the output generated by the Bio.SeqIO.convert function (Biopython toolkit) and I am seeing consistent differences of between 1-2 at low quality. Do you know why this might be happening?

Thanks,
Taylor

[tseemann]

@gittaylor This is probably due to the fact that Solexa originally used a different formula to convert probabilties to Q values, which is described here: http://en.wikipedia.org/wiki/FASTQ_format#Quality
Note how the different formulae only diverge for low qualities. I suspect the Python code is doing a "true" conversion, whereas seqtk is just offsetting the ASCII values.

[lh3]

As @tseemann said. Seqtk is unable to convert Illumina<1.3 fastq to the standard fastq.