VIRify
Version 1

Workflow Type: Common Workflow Language

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.

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SEEK ID: https://dev.workflowhub.eu/workflows/112?version=1

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

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	array containing File
krona_plots	n/a	n/a	array containing 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	array containing File

Version History

Version 1 (earliest) Created 3rd Jun 2020 at 12:04 by Laura Rodriguez-Navas

Added/updated 1 files

Open master 2714822

Creators and Submitter

Creators

Not specified

Additional credit

Martín Beracochea

Submitter

Laura Rodriguez-Navas

License

Apache License 2.0

Activity

Views: 2076 Downloads: 309

Created: 3rd Jun 2020 at 12:04

Last updated: 8th Jun 2020 at 11:21

VIRify Version 1