charcoal analysis of single assembly file

[gaworj]

Hi,

Can I use charcoal to decontaminate single assembly file? I have eukaryotic genome assembly with potential microbial contamination. Unfortunately this is completely new eukaryotic species so I don't know which contigs belong to Eukaryota.

Bests,
Jan

[taylorreiter]

Hi Jan, yes, this should work! Charcoal only throws things out that confidently match against things in the database (by default, GTDB so bacteria and archaea). So all of your eukaryotic contigs will be marked as "clean", while anything that looks like archaea or bacterial sequence will be marked as "dirty".

[gaworj]

Hi,

OK. But can I run it without lineages csv file?

[taylorreiter]

Ah great question! In the lineage CSV file, you can put Eukaryote as the domain and leave the rest of the lineage blank