Assembly oxford nanopore data

Question

[A_heath]

Hi,

I have raw data collected from Oxford Nanopore sequencing of a bacterial genome. These data consist of multiple fastq files. What easy to use tool would you recommend to assemble these raw reads?

Thank you for your help!

Audrey

Answer 1

[colindaven]

Flye is available on Galaxy or on Bioconda if you want a user friendly and simple yet performant tool.

Edit - you can combine the fastq files _before_ assembly with eg the linux cat cmd.

[A_heath]

Thank you for your quick reply. I have an issue because I have multiple raw fastq files in a folder and when I type this command line:

flye --nano-corr /home/.../fastq_folder --out-dir /home/.../output --threads 4

the fastq file extension is not recognized ... Do you have any idea on how to solve this, please ?

edit: I find a way using :

flye --nano-corr /home/.../*.fastq --out-dir /home/.../output --threads 4

Thanks again for your help