There are several tools for this task, I personally like BlobTools for assembled draft genomes. Here is what you get:
I am plagiarizing myself (Interpreting mapping contaminants):
I like to use BlobTools (blasting against NCBI NT) to explore the taxonomic assignment of an assembly, and detect possible contamination - that is, I check for contaminants post-assembly.
You can also use sketches to analyse contamination either on your raw data (pre-assembly) or on assemblies, see:
Mash Screen: what's in my sequencing run?
What’s in my metagenome?
Tool: BBSketch - A Tool for Rapid Sequence Comparison
Finally, you can also use kmer screening tools like Kraken or Centrifuge to screen and filter out contaminants.
modified 5 months ago
5 months ago by
h.mon ♦ 25k