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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 |
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virsorter_virome | n/a | Set this parameter if the input fasta is mostly viral. See: https://github.com/simroux/VirSorter/issues/50 |
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virsorter_data_dir | n/a | VirSorter supporting database files. |
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add_hmms_tsv | n/a | Additonal metadata tsv |
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hmmscan_database_dir | n/a | HMMScan Viral HMM (databases/vpHMM/vpHMM_database). NOTE: it needs to be a full path. |
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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) |
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img_blast_database_dir | n/a | Downloaded from: https://genome.jgi.doe.gov/portal/IMG_VR/IMG_VR.home.html |
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mashmap_reference_file | n/a | MashMap Reference file. Use MashMap to |
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pprmeta_simg | n/a | PPR-Meta singularity simg file |
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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 |
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virfinder_output | n/a | n/a |
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virsorter_output | n/a | n/a |
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high_confidence_contigs | n/a | n/a |
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low_confidence_contigs | n/a | n/a |
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parse_prophages_contigs | n/a | n/a |
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high_confidence_faa | n/a | n/a |
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low_confidence_faa | n/a | n/a |
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prophages_faa | n/a | n/a |
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taxonomy_assignations | n/a | n/a |
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krona_plots | n/a | n/a |
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krona_plot_all | n/a | n/a |
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blast_results | n/a | n/a |
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blast_result_filtereds | n/a | n/a |
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blast_merged_tsvs | n/a | n/a |
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mashmap_hits | n/a | n/a |
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Version History
Version 1 (earliest) Created 3rd Jun 2020 at 12:04 by Laura Rodriguez-Navas
Added/updated 1 files
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master
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Creators and Submitter
Creators
Not specifiedAdditional credit
Martín Beracochea
Submitter
License
Activity
Views: 2166 Downloads: 339
Created: 3rd Jun 2020 at 12:04
Last updated: 8th Jun 2020 at 11:21
Attributions
None