I like BlobTools for checking assembly contamination, it combines blast results, read mapping coverage and GC content to explore possible contaminants. There is also a BlobTools2, but I've never used it - by its description, it is nicer than the previous version. BlobTools is a post-assembly evaluation tool.
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
Also pre- and post-assembly, you can also use kmer screening tools like Kraken, CLARK or Centrifuge to screen and filter out contaminants.
modified 4 weeks ago
4 weeks ago by
h.mon ♦ 30k