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AnantharamanLab / VIBRANT

Virus Identification By iteRative ANnoTation
GNU General Public License v3.0
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Input files for VirSorter and VIBRANT #64

Open maocheng2020 opened 2 years ago

maocheng2020 commented 2 years ago

Hi! I want to ask a question, I see that VirSorter input is contig, VIBRANT input is Scaffold, are the two input different? There is a comparison of the two results in your manuscript, but I didn't find a description about the input file. For me, the result of idba_ud has contig and scaffold, the result of MEGAHIT is only contig, I cat the two contig results together as VirSorter input.But I see that the VIBRANT input file is Scaffold, so the contig result of cat together cannot be used as VIBRANT input? Sorry to bother you, I look forward to your reply. Thanks！

KrisKieft commented 2 years ago

For most purposes feel free to use either. The difference between contig and scaffold won't make an impact on the input format for VirSorter or VIBRANT. They will each work the same with the format that you have (contig or scaffold).

Kris

maocheng2020 commented 2 years ago

@KrisKieft Thanks for your quick reply,can I understand that contig as input to VIBRANT is also correct? The manual of VIBRANT writes scaffold as input, but I want to use the result (contig) of MEGAHIT directly as the input file of VIBRANT. This confuses me. Thanks!

KrisKieft commented 2 years ago

Contigs from Megahit or contigs from any other assembler will work.