We tend to use our nanopore data in conjunction with nanopolish. Unfortunately that requires that the input read matches exactly the k-mer table in the FAST5 file to work. Therefore the adaptor trimming option is not compatible.
As a workaround I made this additional command line option --untrimmed to use the barcode demultiplexing functionality without the adaptor trimming functionality.
An additional refinement i just thought about might be to keep the adaptor trimming but soft mask the characters with lower case, that might be easier for nanopolish to support in future.
Hi Ryan
Many thanks for Porechop, it is great.
The barcode demultiplexing option is very useful.
We tend to use our nanopore data in conjunction with nanopolish. Unfortunately that requires that the input read matches exactly the k-mer table in the FAST5 file to work. Therefore the adaptor trimming option is not compatible.
As a workaround I made this additional command line option --untrimmed to use the barcode demultiplexing functionality without the adaptor trimming functionality.
An additional refinement i just thought about might be to keep the adaptor trimming but soft mask the characters with lower case, that might be easier for nanopolish to support in future.
I hope you will consider this pull request.
Best Nick