Problems with whole genome sequencing

[Blob]

Hi! Some one here who can answer me on how to deal with heterozygosity, repeats and polyploidy when it comes to Whole genome sequencing.
Which techniques are made to deal with these?

Im having some difficulties

Thanks!

[Jackken]

Do you mean loss of heterozygosity?

[Blob]

No, the presence of heterozygosity

[pallevillesen]

Some of it is taken care of be the various assemblers.

Repeats etc. are identified and distinguished by large insert libraries.

If you have extremely high heterozygosity, it may be a problem to make scaffolds.

I don't know you the various algorithms deal with polyploidy.

All these three "problems" should be possible to identify from a kmer plot. If you have a single peak at the expected depth you're fine.

If you also have a large peak with higher depth you have a lot of repeats.

If you also have a large peak with lower depth you have high heterozygosity.

I hope this helps...