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NextSeq auto-detect seems incomplete
Hi,
first of all, thank you for developing the software!
I ran it on some samples that were sequenced with a NextSeq 2000. For some samples, the reads are mostly composed of "G", which is something we need to look into, so this is not the issue :)
The issue is that the autodetection seems to fail, hence the --trim_poly_g
needs to be specified manually as it is otherwise not enabled.
When I look at https://github.com/OpenGene/fastp/blob/ca559a71feed94e74ea449e7567d0506de48dea4/src/evaluator.cpp#L25, the prefixes that are used to identify the machine are very limited.
Specifically, the FASTQ files, I have, start with @VH
for the readnames.
That prefix is, however, not in the list.
Maybe because these prefixes were for NextSeq 5xx and not NextSeq 2000?
Best wishes and stay safe,
Cedric