Greetings, as the title says, I am looking for any tool that can help identify any contaminating contigs in my new genome assembly and filter those contigs. I have tried bloobtool 2 before (which consists of DiamondBlast against uniprot & Blastn against nt database) , but I am not sure if the blob result is reliable since it does not show any bacterial taxonomic hits:
The developer explains it just shows the genome contains no bacterial contamination. I would like second tool to confirm that. Any suggested online tool that can quickly help me identify the contaminating contigs? so I don't need to spend amounts of time building database
1 answer
The method I use to filter out contamination is described by me here: A: How can I remove contaminants from an assembled genome? . If there are so many contigs that Blastn takes too much time, I will use Megablast. It's less sensitive, but faster.
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