Assembly issues

Question

[anna]

I’m trying to assemble reads using spades on galaxy.org. spades but I get a mistake. from the fastqc of the reads I noticed that they have residues of the universal illuminates adapters used for sequencing. I tried to clean the sequences by inserting on trimmomatic also the adapters provided by the company, but I still have spades error. Do any of you know how I could solve the problem and assemble the reads?

Thanks, Anna

[GenoMax]

Please post galaxy related help questions on their help forum for prompt response: https://help.galaxyproject.org/

They can see your data on galaxy and should be able to provide direct help.

Answer 1

[chen]

Trimmomatic hasn't been updated in 5 years, probably you can try fastp? fastp is much faster, simpler, more accurate with more functions. fastp is still being actively developed.

https://github.com/OpenGene/fastp