Automate fasta sequence ordering based on reference

Question

[ThePresident]

Let's say I de novo assembled several bacterial genomes following sequencing. I have scaffolds with a few large contigs in each fasta file. Is there a way to re-order sequences based on a references? I can do this manually for small number of genomes but some automation would be ideal.

The question has been asked before however, the answer wasn't elaborate.

TP

[GenoMax]

mauve has contig mover: https://darlinglab.org/mauve/user-guide/reordering.html

[ThePresident]

Yes, I just realized this as well. Thank you. Non-Mauve solutions also welcome if anyone has ideas.

Answer 1

[colindaven]

Depends on your data - if you have big contigs Medusa will probably work, with many smaller contigs you'll run into trouble. Mike Schatz' lab had a much newer one for eukaryotes but I forget the name.

Theres a couple of older ones called Medusa and chromosomer.

Has anyone used MeDuSa: a multi-draft based scaffolder

Scaffolder with better performance specs