Automate fasta sequence ordering based on reference
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24 months ago
ThePresident ▴ 180

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

reference denovo assembly contigs • 881 views
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Yes, I just realized this as well. Thank you. Non-Mauve solutions also welcome if anyone has ideas.

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24 months ago

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

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