Hybrid assembly SPAdes (Ox. Nanopore + Illumina)

Question

[A_heath]

Hi all,

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!

Audrey

[Kumar]

Hi, Similarly, I am looking to make hybrid assembly of a viral genome. I have got (R1 and R2) and a merged file fastq, generated from Nanopore. Could you please let me know if you have figured out the work flow.

Answer 1

[samuel.a.odonnell]

It might work well enough, you'll see by the output. But if the assembly isnt both complete and contiguous and you have enough coverage, assemble with nanopore and finish polishing with illumina. For that, find an assembler suited to long-read assembly.

[colindaven]

Exactly as Sam above says, try the Flye assembler first, then follow up with multiple rounds of racon, pilon or others for the Illumina polishing.