How to provide paired end short reads to RagTag correct?

[ceanothus]

Hi there,

How do I format the RagTag correct command to receive paired end short reads for validation? Would it be like:

ragtag.py reference query -R forward_reads.fasta -T sr -R reverse_reads.fasta -T sr

or would I have to merge the two files into one?

Thanks.

[VictorCalderon]

Hello,

Would it be okay to assemble these reads into larger contigs? If I am not mistaken, the issue with your approach is that you're trying to pass reads directly to RagTag instead of contigs. As you may know, scaffolding is a process where contigs are aligned to a reference genome, and RagTag is an ideal tool for this.

I would first run an assembler on my reads, like SPAdes or MEGAHIT, to produce a single file with my longer contigs. Then, pass all of those to RagTag directly. You mentioned merging these two files, if you still prefer to do this, read this Biostars thread to understand the perils and possible tools you could use.

Please let us know if you have any questions on how to perform these processes.