Hello,

I was trying to access the similarity between the fastq files generated by bclconvert(3.9) from bcl2fatq(v2). Two adapter sequences were specified according to https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html All the other parameters were default.

I observed that there was a difference in the way the Adapters were trimmed and how the resulting bases were masked. One change which was noted in the https://support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html document was about the Adapter Matching Algorithm which was defaulted to FindAdaptersWithIndels in bcl2fastq and is defaulted to sliding window in bcl convert.

When I ran, bcl2fastq with sliding window approach, the fastq files were exactly same as that of bcl-convert.

Questions:

1. Is there a way to implement FindAdaptersWithIndels with bcl-convert even though the tool currently doesn't support it?

Thanks in advance!