Run abacas for multiple scaffold (20k +)

Question

[Mbillah]

I have a scaffold.fa file which contains more than 20K scaffolds. Now I want to run abacas among them. Abacas wants a single query sequence. But I have more than 20,000 sequences scaffolds. So this is not possible to do one by one. How can I do this?

[Ram]

Please read rules 2 and 6 here: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202