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Check contamination in assembly

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

rna-seq genome next-gen
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updated by onestop_data onestop_data • written by Mehmet Mehmet

2 answers

These are some really good tools:

Metawatt

CheckM

(PHYL)AMPHORA

• 0 views • link
written by dago dago

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

• 0 views • link
written by onestop_data onestop_data

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