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viga (version 0.10.3)

(Viral) contigs to annotate:

Input file as a FASTA file. It can contain multiple sequences (e.g. metagenomic contigs)

RFAM database used for ribosomal RNA prediction:

Metadata of the contigs:

Modifiers per every FASTA header according to SeqIn (https://www.ncbi.nlm.nih.gov/Sequin/modifiers.html)

GenBank division (--typedata):

Number of GenBank translation table (--gcode):

Read length (--readlength):

Read length for the circularity prediction

Window size (--windowsize):

Window size used to determine the origin of replication in circular contigs according to the cumulative GC skew

sliding window size (--slidingsize):

Sliding window size for the origin of replication prediction

Locus tag prefix (--locustag):

Name of the sequences. If the input is a multifasta file, please put a general name

Print the output also as GFF3 file:

Printing the output as GFF3 file (Default: FALSE)

Blast e-value threshold:

Use PHMMER to predict protein function using HMM:

PHMMER database to use for protein function prediction:

PHMMER e-value threshold:

Use DIAMOND instead of BLAST to predict protein function:

DIAMOND database:

DIAMOND Protein Database that will be used for the protein function prediction

Minimum contig length to be considered in the output:

ID threshold:

Coverage threshold:

Max allowed difference between the ID percentages of BLAST and HHSEARCH:

Minimum repeat length for CRISPR detection (--minrepeat):

Maximum repeat length for CRISPR detection (--maxrepeat):

Minimum spacer length for CRISPR detection (--minspacer):

Maximum spacer length for CRISPR detection (--maxspacer):

Use exhaustive BLAST (--blastexh):

Use of exhaustive BLAST to predict the proteins by homology according to Fozo et al. (2010) Nucleic Acids Res (Default=FALSE)

About VIGA

VIGA is a script written in Python 2.7 that annotates viral genomes automatically (using a de novo algorithm) and predict the function of their proteins using BLAST and HMMER.

About this Galaxy wrapper

Requirements

Docker should first be installed and working on the server where this Galaxy instance is setup. The user running Galaxy should be part of the docker user group.

Download or clone the VIGA Github repository (as a submodule) in to the tools directory.

Configuration

Update database paths in .loc files

Edit the following files in the tool-data directory and add paths to corresponding databases:

viga_blastdb.loc
viga_diamonddb.loc
viga_rfamdb.loc
viga_hmmdb.loc

Create or update the Galaxy job configuration file

If the file config/job_conf.xml does not exist, create it by copying the template config/job_conf.xml.sample_basic in the Galaxy directory. Then add a Docker destination for viga. Change /data/databases under docker_volumes to the location where your databases are stored. Here is an example:

<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
<job_conf>
    <plugins>
        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
    </plugins>
    <handlers>
        <handler id="main"/>
    </handlers>
    <destinations default="local">
        <destination id="local" runner="local"/>
        <destination id="docker" runner="local">
                <param id="docker_enabled">true</param>
                <param id="docker_sudo">false</param>
                <param id="docker_auto_rm">true</param>
                <param id="docker_volumes">$defaults,/data/databases:ro</param>
        </destination>
    </destinations>
    <tools>
      <tool id="viga" destination="docker"/>
    </tools>
</job_conf>

Restart Galaxy. The tool will now be ready to use.

Output files

VIGA creates the following output files:

tbl - Table file with all protein information.
gbk - GenBank format file with annotations.
fasta - FASTA format file for GenBank submission
csv - Table file for GenBank submission.
gff - GFF3 format file (if option is selected)

License and citation

VIGA and this Galaxy wrapper - GPLv3.

Galaxy

Goecks, J, Nekrutenko, A, Taylor, J and The Galaxy Team. "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences." Genome Biol. 2010 Aug 25;11(8):R86.
Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. "Galaxy: a web-based genome analysis tool for experimentalists". Current Protocols in Molecular Biology. 2010 Jan; Chapter 19:Unit 19.10.1-21.
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A. "Galaxy: a platform for interactive large-scale genome analysis." Genome Research. 2005 Oct; 15(10):1451-5.

You can use this tool only if you agree to the license terms of: VIGA.