Tool:Giant Virus Finder - discover giant virus sequences in metagenomes

Question

[Csaba Kerepesi]

We have developed a pipeline tool to find giant virus sequences in metagenomes. It called Giant Virus Finder and are available from the site of our group: Giant Virus Finder. This is the only tool specialized to find giant viruses.

Using it we have found giant virus sequences in metagenomes sampled from the saline desert of Kutch (Giant viruses of the Kutch Desert) and from Antartic dry valley (The "Giant Virus Finder" Discovers an Abundance of Giant Viruses in the Antarctic Dry Valleys). These results are important because nobody have found giant viruses in soil samples of a dry environment before us.

A very interesting side product of the Giant Virus Finder is Giant Virus Toplist.

If you want to know more about these interesting organsims I also recommend this site.

I welcome any comment, question and suggestion. This will be the official support topic of the tool.

[vmevada102]

Is this tool available in Galaxy?

This tool is important to identify the Giant Viruses from Metagenomes.

[Csaba Kerepesi]

thank you for your comment. As I know Giant Virus Finder has not been available via Galaxy, yet. I am going to send an email to Galaxy support asking them about this issue.

[vmevada102]

Hello i am having problem with installation in Ubuntu 16 .

I have received error during installation. Please help me to resolve it.

[Csaba Kerepesi]

If you want to create a new Giant Virus Toplist by "TopgiantsEntrez.py", you need to install Biopython 1.5 or later. For more details please check the README file of Giant Virus Finder.

However, if you want to use the Giant Virus Toplist published by us, you do not need to install Biopython and run "TopgiantsEntrez.py". Simple download the giant virus toplist file and skip this step in the workflow described in the README.

I will update the Giant Virus Toplist soon (the current version is generated 3 years ago).

[vmevada102]

Thank you Csaba Kerepesi

If possible, kindly update the Giant virus toplist file. As i have got total Nearly 200+ viral genome from ncbi. I had installed the Biopython, still facing problem to run script as described in previous post.

[Csaba Kerepesi]

I have updated the Giant Virus Toplist, and the input file of the Giant Virus Finder. The problem was caused by the structures of the data were changed in Entrez/Biopython, but now I've fixed the problem, and update the scripts TopGiantsEntrez.py and TopGiants.pl).

[vmevada102]

Need little more support again. After completion of First step Blast.

***Giant Virus Finding, Phase1:
- mkdir Giants-in-16Soil-metagenomes
- perl Phase1Blast-MultiCore.pl Giants-in-16Soil-metagenomes > Giants-in-16Soil-metagenomes/log-Phase1Blast-MultiCore.pl.txt
- perl Concat.pl Giants-in-16Soil-metagenomes

Upton here every thing has been run smoothly. But afterwards, when i am trying to run following command too extract candidate sequences, it gives **blank file.**

perl GetCandidateReads.pl Giants-in-16Soil-metagenomes 16SoilMetagenome

While the results may have several sequences as output in phase1-out directory.

Kindly guide me to resolve the issue.

[Csaba Kerepesi]

Hi,

Thank you for the question!

Do you use any input sequences (e.g. the fasta files of the 16 soil metagenomes?).

Best, Csaba

[Csaba]

Finally, we solved the issues and updated the software (https://pitgroup.org/public/giant-virus-finder/latest/). Giant Virus Finder, now, fits the changed BLAST outputs

Answer 1

[Csaba Kerepesi]

Giant Virus Toplist is updated. It is interesting that the number of giant viruses (more exactly: the viruses having a genome sequence larger than 300000 bp) almost doubled over the last three years. The leader is still Pandoravirus salinus with 2.47 million bp, but there are new members in the top 5: Pandoravirus inopinatum (2.24 million bp), Tupanvirus deep ocean (1.51 million bp), Orpheovirus IHUMI-LCC2 (1.47).

A printscreen with the top5: