Racon command line with paired-ends Illumina reads

Question

[A_heath]

Hi all,

I have a draft assembly using long reads only with Flye of a small bacterial genome (820,000 bp).I would like to improve this assembly with paired-end Illumina reads using Racon.

However, in the command line of Racon, I don't see how I can enter both Illumina files (R1.fastq and R2.fastq).

racon [options ...] <sequences> <overlaps> <target sequences>

Could I have some help, please?

Thank you!!

Audrey

[tothepoint]

Probably you need to convert this into sam file first and follow the command:

racon  [Illumina Joined] [sam] [unpolished contigs]  > [polished contigs] 

[A_heath]

Thank you so much for your reply. I've already generated the alignement file using bowtie2. I was just wondering how to join Illumina paired-end reads so that racon take them into consideration ?

[cpad0112]

this should help you: https://github.com/isovic/racon/issues/68. Please pay attention to the last comment of the same post wrt sam file.