Assembler for only nanopore data

Question

[ringourquia]

Hi Everyone! Does anyone know about an assembler where the input is ONLY nanopore data (i.e, no Illumina or any other kind of short reads)? What about using ABySS for assembling only nanopore reads, is it OK? (I know that SPAdes should not be used if I have only nanopore reads)

Thanks a lot!

[Juke34]

Have a look here you will probably find what you want.

Edit by GenoMax: Outdated link corrected.

[jpablo]

I've seen good reviews of Flye for nanonpore data (I never uded it myself).

Prior the the assembler you may user nanoq for quality control https://github.com/esteinig/nanoq and/or Kraken for contamination detection https://github.com/DerrickWood/kraken https://www.youtube.com/watch?v=n-6pH3EPZDI

Answer 1

[Dave Carlson]

I believe Canu is a popular option. Should work for either nanopore or PacBio long read data.

[ringourquia]

Thanks a lot Dave! I will check it out

Answer 2

[Alex]

Flye is working very well for us working on metagenomic nanopore data. Especially, because it offers the --meta parameter with the possibilty to assemble contig of different depth.

Answer 3

[harish]

You can try Canu, Flye, Necat, Minimap-miniasm, Ra etc.

Answer 4

[colindaven]

Shasta is very good and fast, provided you have lots of RAM (over 500 GB for many genomes).