search

ZiyueYang01 / VirID

VirID: An integrated platform for the discovery and characterization of RNA Viruses
MIT License
11 stars 5 forks source link

Support for Contigs File as Input for RNA Virus Identification #13

Closed linzhl1 closed 20 hours ago

linzhl1 commented 21 hours ago

Hi developer,

Thank you for developing VirID, an excellent RNA virus discovery and characterization tool. I have a question regarding the input files for RNA virus identification.

Does VirID only accept raw reads files as input for identifying RNA viruses? If so, would it be possible to add support for contig files assembled by Megahit as input for RNA virus identification?

This feature would benefit users who have already performed assembly and want to use the contigs directly.

Thank you for considering this request!

ZiyueYang01 commented 21 hours ago

You can run it like this:

VirID phylogenetic_analysis -classify_i test/test_contig.fasta \
    -out_dir out_path --threads 90 --keep_dup

The phylogenetic_analysis mode use contigs as input.

linzhl1 commented 20 hours ago

Thank you for getting back to me so quickly.