Question

Automate fasta sequence ordering based on reference

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2.3 years 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 • 949 views

ADD COMMENT • link updated 2.3 years ago by colindaven 6.8k • written 2.3 years ago by ThePresident ▴ 180

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

ADD REPLY • link 2.3 years ago by GenoMax 146k

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

ADD REPLY • link 2.3 years ago by ThePresident ▴ 180

score 0 · Answer 1 · 2022-07-26

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