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abaizan / kodoja

Kodoja: identifying viruses from plant RNA sequencing data
MIT License
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How could I disable and skip the trimmomatic step? #33

Closed coralzhang closed 5 years ago

coralzhang commented 5 years ago

How could I disable and skip the trimmomatic step?

peterjc commented 5 years ago

Simple answer, provide FASTA not FASTQ as input:

https://github.com/abaizan/kodoja/blob/kodoja-v0.0.9/diagnosticTool_scripts/kodoja_search.py#L148

Beyond that you could try faking it with relaxed minimum length and an empty adapters file, but ultimately, you would have to modify the code. See also:

https://github.com/abaizan/kodoja/blob/kodoja-v0.0.9/diagnosticTool_scripts/diagnostic_modules.py#L134

coralzhang commented 5 years ago

Thanks!