How to completely align chromosomes/scaffolds from de novo genome assemblies using MUMMER or other tools?

Question

[Drew]

I am having trouble with Mummer and Dgenies to provide me with a nice continuous dot plot. Basically, I have a bunch of de novo assembled genomes from Flye where the number of contigs is essentially to chromosome level. However, some of the entire contigs are inverted, compared to one another or to the reference and I'm not sure how to visualize these on a dotplot as one continuous diagonal ranging from chromosome 1-12. It seems to start the dotplot at an arbitrarily chosen chromosome for each plot rather than being arranged. I'm also not sure how to 'invert' the inverted chromosomes/contigs to correctly fit the dot plot for better visualization. I've also used RagTag. Even if I can't get the contings into the correct orientation, I would like to at least order the dot plot from chromosomes 1-12.

Can anyone give me some advice as to how to tackle this?

Answer 1

[christophe.klopp]

With dgenies you can left click on any alignment square of the dotplot, this will show a local menu, and reverse it using the "reverse" item.

Answer 2

[Michael]

I'm also not sure how to 'invert' the inverted chromosomes/contigs to correctly fit the dot plot for better visualization.

Just reverse complement the sequences that are in opposite orientation to the reference.

Even if I can't get the contings into the correct orientation, I would like to at least order the dot plot from chromosomes 1-12.

There's a Sort contigs button in D-genies. That should sort the contigs in the same order as the reference. Check also, if the reference itself is sorted properly.

[Drew]

I was hoping to avoid manually comlementing specific contigs in a given genome. I've tried both the -layout option and sort contigs option in D-genies and it does not fix the problem. I'm calling it a problem because it makes my visualizations hard to follow.

Answer 3

[cmdcolin]

this blog post has a method for flipping reverse orientation contigs. it is it's own plotting tool instead of dgenies but perhaps could be leveraged http://jmonlong.github.io/Hippocamplus/2017/09/19/mummerplots-with-ggplot2/

Answer 4

[Charles Plessy]

You might be interested in my pipeline (https://nf-co.re/pairgenomealign), which runs last-dotplot in a mode that attempts to flip sequences to diagonalise the plot.