sugestion nanopore assembly and illumina reads

Question

[zion22]

hi I come here because I have a nanopore assembly and illumina reads from the same organism and I wanted to know what you recommend to improve my genome, with these input files.

[GenoMax]

Nextpolish: https://github.com/Nextomics/NextPolish
Pilon: https://github.com/broadinstitute/pilon
Unicycler: https://github.com/rrwick/Unicycler

Answer 1

[predeus]

What is the organism, and what sort of coverage do you have in Illumina and Nanopore? It matters a lot.

If it's a bacteria, it depends on the type of bacteria, but Unicycler works really well for most. If there are lots of repeats though, you might be better of with first assembling it with Flye, and then polishing with Illumina using Racon and then Pilon.

If you're dealing with a eukaryote, you probably want to do the long-read assembly first, and then polish it. There are many assemblers that do a pretty good job. I'd say Flye is the most reliable and requires the least tuning. Canu is good, although a bit slow. Shasta recently impressed me, and wtdbg2 and Raven are all very fast.

[zion22]

but I have a preliminary assembly (nanopore) and other reads (illumina), how can I make this improvement, it is for several bacteria.

[predeus]

You need a program called polisher. Racon works with Illumina reads (you'll need to concatenate paired-end reads for this). After this, Pilon can be used for exhaustive polishing of remaining imperfections.

I would also still give Unicycler a try though - it might produce better assemblies than long-read only with polishing.