I have both Oxford Nanopore and Illumina sequencing data of a bacterial genome. I would like to perform an hybrid assembly combining the two sequencing techniques.
Is SPAdes the most appropriate software to do it?
And, I typed the following command line, is it appropriate for this hybrid assembly?
spades.py -1 R1_001.fastq -2 R2_001.fastq --nanopore combined_files.fastq -o Hybrid_assembly_output
Note that I combined into a single file all the .fastq files obtained from Ox. Nanopore sequencing.
Thank you very much for your advices/help!