Redundancy and contamination analysis on assembly

[medvedevgroup]

Redundancy and contamination analysis on assembly

[iminkin]

Hi,

I think SibeliaZ might be helpful in this scenario, though you will have to find a way to postprocesss the results (or visualize them) to find the roots of the problem.

[pashadag]

Hi Simón,

You can certainly try to use SibeliaZ for this, but as Iila mentioned, you would have to post-process the results. There may be simpler ways to get to the bottom of your problem. For example, for the second issue, you can use BLAT or BLAST to align your scaffolds against the human reference. For the first issue, there might be specialized tools for doing this, for example https://github.com/dfguan/purge_dups.

Good luck with it,
Paul