increase highest possible Q value to comply with Aviti high quality data

[splaisan]

Dear John,

When I run ngmerge on Element Biosciences Aviti data I get the error

Error! Quality scores outside of set range

This is due to the extra quality of the Element Biosciences Aviti which exceeds the classical 0:40 range for Illumina data
Could it please add code to ignore all Qvalues 40+ and set them instead to 40 or enlarge the authorised range to match Aviti data (up to 56! https://docs.elembio.io/docs/bases2fastq/outputs/#quality-scores).

I am now parsing my fastq and downgrading Qvalues to 40 but it would be better to fix NGmerge instead as Aviti is there to stay.

I see a file ngmerge.h with large matrices but do not know what to do with them to add scores up to at least 46 which is my highest measured value on the current data.

Thanks in advance

[jsh58]

I believe this has been addressed before in #4

[splaisan]

Thanks @jsh58 ,
There is indeed info there but as for building new tables from Aviti data, the explanations in your manuscript are far from enough, even with the provided python scripts.
A full tutorial, including R commands would be necessary in order to reproduce this published data.
Could you by any chance share such a full command code so that I can run it on aviti data (we have phiX reads in sequences obtained from Illumina libraries) and produce new tables?
If I succeed in this, I will be happy to contribute the resulting tables here.
Thanks in advance