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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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Input assemblies for COBRA #12

Closed asierFernandezP closed 9 months ago

asierFernandezP commented 10 months ago

Hi,

You mention that COBRA has so far only been tested on assembled contigs from metaSPAdes, IDBA_UD, and MEGAHIT. Would you recommend to use it on viral contigs that have been assembled using single cell mode (--sc) from SPAdes (used in our study for metaviromes)?

Thank you, Asier

linxingchen commented 10 months ago

Hi,

You mention that COBRA has so far only been tested on assembled contigs from metaSPAdes, IDBA_UD, and MEGAHIT. Would you recommend to use it on viral contigs that have been assembled using single cell mode (--sc) from SPAdes (used in our study for metaviromes)?

Thank you, Asier

Hi Asier,

I believe it is ok to use COBRA for your data, please select "metaspades" for the assembler option.

Let me know if you have other questions.

Best, LINXING