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linxingchen / cobra

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
MIT License
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Questions about the application of COBRA #31

Open Xinpeng021001 opened 3 months ago

Xinpeng021001 commented 3 months ago

Dear Linxing,

Good afternoon. Thank you for this excellent paper and tool! I read this paper and shared it with my lab members. I have some questions about the application of COBRA:

  1. For the metaSPAde you mentioned in the README file and paper, have you tested the MetaviralSPAdes(https://academic.oup.com/bioinformatics/article-abstract/36/14/4126/5837667) which is the specific viral mode for assembly? I'm working on some metagenomic data and trying to find the viral sequence in it. I think it would be a little different if we use metaSPAde and then identify viral contigs by other tools like VIBRANT or directly identify viral contigs based on MetaviralSPAdes. I think it could be a similar question with closed#22.

  2. We're working on the Mitochondria sequence also, and do you think COBRA could be used into others like mitochondria sequences, to re-assemble those sequences, using reference genome sequence as input1 and assembled results as input2? Or we have to use those inputs from the same data?

    Thank you for your time and patience!

    Best Regards, Xinpeng

linxingchen commented 3 months ago

Hi Xinpeng,

Thank you for your interest in COBRA.

  1. I know this tool but have not used it. Based on the paper and "We describe a METAVIRALSPADES tool for identifying viral genomes in metagenomic assembly graphs that is based on analyzing variations in the coverage depth between viruses and bacterial chromosomes." I guess it is not better than those viral identification tools like VIBRANT. I will suggest assembling you data using a general metagenomic assembly and then predict viral contigs/scaffolds using something like VIBRANT.

  2. For COBRA, you need the contigs/scaffolds from the same assembly, not anything from outside of assembly, for example, reference genome.

I hope this helps. I am happy to discuss more.

Best, LINXING

Xinpeng021001 commented 3 months ago

Thank you for your reply! I really appreciate your help and work!

Best Regards, Xinpeng