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I have two FASTAs/assemblies of the same species, but the bases are somewhat different. I would like to explore this.
What tools/methods exist to compare two FASTAs and see the difference in structure between them? Are there visualization tools available, something like IGV?
I think users would need to do a multiple-sequence alignment between these FASTAs, and then check for the differences between them. However, I don't know if a "standard approach" exists to do this.
Depending on how long the sequences are, you could use the LAST Web Service:
It has an HTML view that shows base-level differences with colour-coding.
LAST [download / command-line version] can also be used for producing whole-genome comparison dot-plots.
Another thing I do for comparing assemblies is to chop one assembly into smaller pieces (e.g. 10kb), map the pieces to other other assembly to generate BAM output, then look at the BAM pileup file in a BAM viewer (e.g. Tablet).
For whole-genome align: Maybe you could use mummer? Mummer is good to align the whole genome of species, and it also has so many other tools to modify the result. (It can show the SNP.)
For short sequence: You could try mega X
Before you compare your genome assembly fasta, I would recommend you first do a reference guided scaffolding using the tool RagTag.
Once you are done you can compare the newly generated scaffolds (with other genomes or not) using the software BRIG. I made a video of how to use this software here
In addition you can also do a genome annotation on your scaffold using prokka. I made a video for that as well here
Good luck
