How to creating input file : -f "sequences to scaffold" and -s "file-of-filenames"

[Hai1983]

Dear everyone.

I try to use LINKS to scaffolding genome assemblies with long reads (PacBio reads -Hifidata). Now, I have a draft genome with 800 cotigs ~780M and Hifi.fasta file . It very useful, if possible share me example of these data.

Thanks in advance .

Sincerely. Hai

[MurathanGoktas]

Hello,

If your draft genome name is x.fasta input it as -f x.fasta

If you only have one HiFi read dataset, and its name is y.fasta; create a fof file with echo y.fasta >> reads.fof Then input it as -s reads.fof.

Let me know if you have any further questions.

[github-actions[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your interest in LINKS!