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Assembly oxford nanopore data

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

assembly oxford nanopore
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written by A_heath • A_heath

1 answer

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.

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written by colindaven colindaven

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

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written by A_heath • A_heath

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