Comparing two de-novo assembled genomes

[calbertovj]

Hi all,

I would like to compare two fungal genomes that have been sequenced and assembled de novo. These genome are different isolates from the same species but have different genome sizes (33.4Mb and 37Mb). They are haploid. I have predicted the genes for each genome using Maker. I would like to compare these genomes in several ways:

- List of genes that are unique to both isolates and list of genes that are common.
- Detect Structural variation: gene duplication, rearrangement, etc.
- Any other interesting feature ??

Any advise would be highly appreciated since my bioinformatics skills are low. Which software can I use??

[TiborNagy]

Comparing gene names is very simple: use comm command.
Structural variation: map reads back to the genomes and use VariationHunter, SVDetect or other program from this list.