metavisitor_logo

Metavisitor is a user-friendly and adaptable software to provide biologists, clinical researchers and possibly diagnostic clinicians with the ability to robustly detect and reconstruct viral genomes from complex deep sequence datasets. A set of modular bioinformatic tools and workflows was implemented as the Metavisitor package in the Galaxy framework. Using the graphical Galaxy workflow editor, users with minimal computational skills can use existing Metavisitor workflows or adapt them to suit specific needs by adding or modifying analysis modules.

Reference viral database

Metavisitor's workflows use a home-made reference viral database vir2. This database was made using Galaxy-Workflow-Metavisitor__Workflow_for_nucleic_vir2_generation and Galaxy-Workflow-Metavisitor__Workflow_for_proteic_vir2_generation, that can both be found in Metavisitor's Github.

How was nucleic vir2 generated?

  • Downloading every viral sequence from NCBI's nuccore database with the following queries (2018/03/21):

txid10239[Organism] NOT txid131567[Organism] NOT phage[All Fields] NOT patent[All Fields] NOT chimeric[Title] NOT vector[Title] NOT method[Title] NOT X174[All Fields] AND 301:10000[Sequence length]

txid10239[Organism] NOT txid131567[Organism] NOT phage[All Fields] NOT patent[All Fields] NOT chimeric[Title] NOT vector[Title] NOT method[Title] NOT X174[All Fields] AND 10001:1300000[Sequence length]

  • Clustering sequences with 95% identity and shorter than 10 001 bp using vclust.

vir2 is available for download in Figshare

Quick Start

Users who want to use Metavisitor on the Galaxy Mississippi Server, or got already the Metavisitor suite of tools installed in their own Galaxy server, can jump to the next chapter Prepare input data histories.

Availability of Metavisitor tools and workflows

Metavisitor has been developed at the ARTbio platform. Its tools are primarily available in GitHub. Its workflows are primarily available in the metavisitor repository

Metavisitor tools and workflows are also available in the toolshed

Metavisitor tools developed by ARTbio in the ARTbio GitHub

Tools from other developers are used in the suite metavisitor-2. These tools are available from the main Galaxy toolshed:

 name="bowtie2" owner="devteam"
 name="data_manager_bowtie2_index_builder" owner="devteam"
 name="data_manager_fetch_genome_dbkeys_all_fasta" owner="devteam"
 name="fasta_compute_length" owner="devteam"
 name="fasta_filter_by_length" owner="devteam"
 name="fastx_trimmer" owner="devteam"
 name="ncbi_blast_plus" owner="devteam"
 name="data_manager_bowtie_index_builder" owner="iuc"
 name="khmer_normalize_by_median" owner="iuc"
 name="sra_tools" owner="iuc"
 name="trinity" owner="iuc"
 name="vsearch" owner="iuc"
 name="regex_find_replace" owner="galaxyp"
 name="spades" owner="nml"

Availability of Metavisitor tools and workflows for Galaxy instance administrators

All metavisitor tools are available from the suite_metavisitor_2 Galaxy Admin can just install this suite of tools by using the Install new tools menu in their Admin panel, searching for "metavisitor", and installing the suite_metavisitor_2 tool suite.

Galaxy Admins can install the workflows from the metavisitor_workflows repository in the main Galaxy toolshed, which will install in addition all tools needed for Metavisitor.

Availability of Metavisitors workflows for any Galaxy instance user.

We have deposited the Metavisitors workflows in the myexperiment server, where they are searchable with "metavisitor" keyword and can be downloaded and reuploaded to the Galaxy instance.

Starting a Metavisitor Galaxy server from scratch

In the last section of this documentation, we provide instructions to set up Galaxy server instances from scratch with pre-installed Metavisitor tools and workflows: