VIRify
Version 1

Stable

VIRify is a recently developed pipeline for the detection, annotation, and taxonomic classification of viral contigs in metagenomic and metatranscriptomic assemblies. The pipeline is part of the repertoire of analysis services offered by MGnify. VIRify’s taxonomic classification relies on the detection of taxon-specific profile hidden Markov models (HMMs), built upon a set of 22,014 orthologous protein domains and referred to as ViPhOGs.

Inputs

ID Name Description Type
input_fasta_file n/a n/a File
virsorter_virome n/a Set this parameter if the input fasta is mostly viral. See: https://github.com/simroux/VirSorter/issues/50 boolean
virsorter_data_dir n/a VirSorter supporting database files. Directory
add_hmms_tsv n/a Additonal metadata tsv File
hmmscan_database_dir n/a HMMScan Viral HMM (databases/vpHMM/vpHMM_database). NOTE: it needs to be a full path. Directory
ncbi_tax_db_file n/a ete3 NCBITaxa db https://github.com/etetoolkit/ete/blob/master/ete3/ncbi_taxonomy/ncbiquery.py http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html This file was manually built and placed in the corresponding path (on databases) File
img_blast_database_dir n/a Downloaded from: https://genome.jgi.doe.gov/portal/IMG_VR/IMG_VR.home.html Directory
mashmap_reference_file n/a MashMap Reference file. Use MashMap to File?
pprmeta_simg n/a PPR-Meta singularity simg file File

Steps

ID Name Description
fasta_rename Filter contigs
length_filter Filter contigs Default lenght 1kb https://github.com/EBI-Metagenomics/emg-virify-scripts/issues/6
virfinder VirFinder
virsorter VirSorter
pprmeta PPR-Meta
parse_pred_contigs Combine
prodigal Prodigal
hmmscan hmmscan
ratio_evalue ratio evalue ViPhOG
annotation ViPhOG annotations
assign Taxonomic assign
krona krona plots
fasta_restore_name_hc Restore fasta names
fasta_restore_name_lc Restore fasta names
fasta_restore_name_pp Restore fasta names
imgvr_blast Blast in a database of viral sequences including metagenomes
mashmap MashMap

Outputs

ID Name Description Type
filtered_contigs n/a n/a File
virfinder_output n/a n/a File
virsorter_output n/a n/a Directory
high_confidence_contigs n/a n/a File?
low_confidence_contigs n/a n/a File?
parse_prophages_contigs n/a n/a File?
high_confidence_faa n/a n/a File?
low_confidence_faa n/a n/a File?
prophages_faa n/a n/a File?
taxonomy_assignations n/a n/a {"type"=>"array", "items"=>"File"}
krona_plots n/a n/a {"type"=>"array", "items"=>"File"}
krona_plot_all n/a n/a File
blast_results n/a n/a File[]
blast_result_filtereds n/a n/a File[]
blast_merged_tsvs n/a n/a File[]
mashmap_hits n/a n/a {"type"=>"array", "items"=>"File"} (Optional)
help Creators and Submitter
Creator
  • Martín Beracochea
Submitter
Activity

Views: 257   Downloads: 5

Created: 3rd Jun 2020 at 12:04

Last updated: 8th Jun 2020 at 11:21

Last used: 27th Nov 2020 at 05:59

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