Detecting genomic rearrangements from resequencing

Question

[ThePresident]

Hello,

I have sequenced a bacterial genome (Illumina, paired-end), got around 20M reads and I did de novo assembly which yielded near 100 contigs greater than 1kb. Now, I have good reasons to suspect that this particular strain underwent major genomic rearrangement such as large inversions, duplications, deletions etc.

Now, what would be the best way to detect these genomic rearrangements (compared to the reference genome from NCBI)?

Thanks,

TP

[microfuge]

Synmap (link here) from coge is a good tool.

[ThePresident]

Indeed, not a bad tool. However, I am having bad time interpreting its results. All my contigs are upside down (which I would expect as they are assembled randomly) but only one contig seems "broken" (one part of the contig mapping to one part of the genome and the other part mapping elsewhere). Perhaps, my initial assumption was wrong unless I am interpreting this in a wrong way?

Answer 1

[ThePresident]

This probably shouldn't go to the answer section, but just in case someone else is looking to do a similar mapping: here's a great tool that helped me visualize contig orderings. And here's the original paper:

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0381-3