Automate fasta sequence ordering based on reference
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.
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colindaven
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ThePresident
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ThePresident
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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.
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mauvehas contig mover: https://darlinglab.org/mauve/user-guide/reordering.htmlYes, I just realized this as well. Thank you. Non-Mauve solutions also welcome if anyone has ideas.