Can I use a multi-fasta reference file with Scaffold_builder?

[andrea...@googlemail.com]

I want to use Scaffold_builder for a newly sequenced genome. For the closest reference however only a genomic draft is available comprised of ~380 scaffolds. Will Scaffold_builder treat these scaffolds properly if I use them as the reference (multi-fasta file) or do I have to stitch them together with Ns?

[Geni]

Hi Andrea,

Unfortunately scaffold_builder does not work using a reference with multiple sequences; you have to stitch them together with Ns or try to find a reference which is a complete genome.

Let me know if you have some other question

Take care