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Assembler for only nanopore data

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!

genomics assembly ont abyss
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updated by GenoMax GenoMax • written by ringourquia • ringourquia

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

Edit by GenoMax: Outdated link corrected.

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updated by GenoMax GenoMax • written by Juke34 Juke34

4 answers

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

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written by Dave Carlson Dave Carlson

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.

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written by Alex • Alex

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

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written by harish harish

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

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written by colindaven colindaven

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