Rotate circular contigs to replication initiator protein (ex. dnaA, repA)

Question

[SergeW]

Hi all,

I'm currently having issues trying to compare hybrid de novo assemblies of bacterial isolates to a reference genome (Using tools like Mauve, QUAST etc.). This because of the rotation/orientation of the contigs. I would like to know what the best (and easiest) way is to rotate my circular contigs from my polished Flye assembly to start at a dnA or repA protein (just like Unicycler does).

What my assembly looks like using Flye long-read assembly + Additional polishing

What my assembly looks like using Unicycler in hybrid mode.

Thanks in advance.

[SergeW]

I think I have solved the problem using Circlator's fixstart option.I still have to look into the program whether it works the way that I want but it seems promising.

[rthapa]

Hi, were you able to fix the issue with Circlator?

[SergeW]

Hi Rthapa, Yes, Circlator helped me to make assembly-reference comparisons (Ex. Mauve) easier when the starting point is different for both fasta files.

[rthapa]

Thank you. Did you try calling structural variants after fixing the start point. If so did you use mauve for calling SV?

[SergeW]

I did not focus on calling Structural Variants but I think Mauve and MUMmer are ways to easily identify SVs. By having your assembly and reference at the same starting point makes the alignment more clear. This example from alex.zaccaron https://ibb.co/ct35NDQ (Look at C) shows what happens if your assembly has a different starting point than your reference genome. I'm not 100% sure whether a shift in contig starting point is necessary but I think it makes comparison between your assembly and reference easier. Have a look at this post.