Check contamination in assembly

Question

[Mehmet]

Dear all:

I would like to ask you which program you use to check contamination in assemblies. As you know, especially in metagenomics and meta transcriptomics work, it is highly possible to get contaminated sequences from other organisms apart from target organism. I used prodege tool to check contamination. I was wondering which tools are also used for this.

Best

Answer 1

[dago]

These are some really good tools:

Metawatt

CheckM

(PHYL)AMPHORA

Answer 2

[onestop_data]

Here is a CheckM tutorial for contamination and completeness if needed.