viralVerify

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When running viralverify, an output file "XXX_input_with_circ.fasta" is produced for input XXX.fasta. However, this file contains the same number of sequences as the input. Exploring the repo, I noticed it...

jnesme

How to run this tool?

3

I'm working on an institute-wide pipeline for JCVI and had some trouble running your tool. Here's my version installed via pip: ``` viral_verify --version viral_verify, version 0.1.1 ``` Here's my...

jolespin

Since the cutoff used for plasmid prediction differs to that one used in plasmidVerify, viralVerify outputs lots of plasmid sequences as unknown. Cutoff selection for plasmid prediction should be improved.

Dmitry-Antipov

Plasmids classified as viruses

4

Consider the attached FASTA file. It contains two sequences that match a plasmid from RefSeq at 99% IDY. However, there are classified as virus by viralVerify. Looks strange. [ic5-metaplasmidspades.plasmid.fasta.zip](https://github.com/ablab/viralVerify/files/5545608/ic5-metaplasmidspades.plasmid.fasta.zip)

asl