Usage of cobra - Githubissues

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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Usage of cobra #25

Open quliping opened 6 months ago

quliping commented 6 months ago

Cobra is an interesting software, but I have some questions. Is the input data must be viral metagenome data? I'm not sure if cobra could works for common metagenome data and will cobra produce some bacteria or archaea MAGs? Thanks.

linxingchen commented 6 months ago

Hi, thanks for your interest in COBRA. Could you please refer to Issue#22 regarding the usage of COBRA on whole metagenomes? Let me know if anything stated therein is unclear.

Best, LINXING

linxingchen commented 6 months ago

Technically, you could use COBRA before binning, this step will make some of your contigs/scaffolds longer, but the issue is you have to rerun the mapping for a new sequencing coverage profile.