domains / families / science / contamination-detection

contamination-detection

separate

Detects and removes contamination in genome assemblies via two disjoint workflows - foreign-sequence screening of a single-organism (eukaryote/isolate) assembly with NCBI FCS-GX (GenBank-submission-mandatory), FCS-adaptor, and BlobToolKit blob plots; and MAG/bin quality assessment with CheckM2 plus GUNC (chimerism) plus GTDB-Tk taxonomy, judged against MIMAG. Covers why CheckM2 alone is blind to disjoint-marker chimeras, the FCS-GX RAM wall, organelle/NUMT triage, strain heterogeneity, and the HGT-vs-contamination (tardigrade) trap. Use when screening an assembly for foreign contamination before GenBank submission, assessing MAG completeness/contamination/chimerism, deciding which contigs to remove, or distinguishing real HGT from contaminant contigs.

When to use

• screening an assembly for foreign contamination before GenBank submission
• assessing MAG completeness, contamination, and chimerism
• deciding which contigs to remove
• distinguishing real HGT from contaminant contigs
• foreign-sequence screening of a single-organism assembly
• MAG/bin quality assessment
• organelle/NUMT triage
• strain heterogeneity analysis

When not to use

• running CheckM2 on a eukaryotic nuclear assembly
• running FCS-GX on a single MAG to determine MIMAG contamination percentage

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