Nanopore support

[arunvv90]

I have run the Falco using the following commands
falco --nano reads.fastq.gz
I am using nanopore reads. Html report says it is using the sanger/illumina encoding even though I have specified the nanopore. Do I need to change anything else. Publication says falco has been tested with both Illumina and nanopore data. Does falco supports the following for nanopore reads
-Q score of nanopore instead of Illumina phread score

• Does it detects the adapter or barcodes of nanopore reads
• Does it supports the overrepresentation feature for nanopore reads

summary.txt
fastqc_data.txt

[Hedi65]

i have the same problem

[guilhermesena1]

Hi,

The "Sanger/Illumina" is currently hard-coded into the report, I am working on the next release to address this issue and print the correct encoding when --nanopore option is set. That said, all the modules should work the same regardless if reads are from Illumina or nanopore. Specifically, per-base sequence content, adapters, quality distribution, overrepresented sequences etc. can still be interpreted the same way even if the encoding says Illumina. I apologize sincerely for the confusion!

[andrewdavidsmith]

@guilhermesena1 @arunvv90 I'm wondering if this issue is about the html, the documentation, or something wrong in the function of falco? @Hedi65 Can you clarify which same problem? Is it lack of information, uncertainties, the wrong name in the HMTL output?