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News

 Current news: 
A maintenance event is scheduled on Metavir computing cluster, so the upload of new projects will be stopped on July 27th and 28th. Results visualization for projects already uploaded should not be impacted.

The Metavir Team



By sroux on 2016-07-26.
 Older news: 
Title Compute nodes issue
News

Dear Metavir users, The computing cluster hosting Metavir had some temporary issues in the last weeks, leading to failed jobs (e.g. phylogenetic trees or taxonomic compositions coming back with 0 sequences). We are working actively on a fix for these problems, and re-launched all the jobs we identified as failed. However, if you come across any unexpected result, please notify us so we can re-run the analysis if needed. We are deeply sorry for the inconvenience, and hope to solve this as soon as possible. The Metavir Team


By sroux on 2015-06-05.
Title Upload re-opened
News

Dear Metavir users, The upload of new viromes to Metavir is now possible again. Thank you for your patience, and please let us know if you experience any trouble or unexpected behavior. The Metavir Team


By sroux on 2015-04-01.
Title Upload shutdown
News

Dear Metavir users, Due to a saturation of Metavir storage space and computing capacities, we had to stop the upload of new projects. We are currently working to get the server back to normal, and hope to reinstate the upload of new projects as soon as the infrastructure issues are fixed, and when projects remaining in the queue will have been processed. The storage issue may also have impacted some of the recently uploaded projects, by providing incomplete results. We tracked down and removed all the ones we could identify, but please let us know if you encounter any weird result for one of your recent project, like for example an unusually low number of BLAST hits in the taxonomic composition, and we will look into it. Stay tuned for updates on Metavir in the next days or weeks (with hopefully the recovery of the server full capacity). The Metavir Team


By sroux on 2015-02-26.
Title Kmer comparison
News

Comparison based on di-, tri- and etra-nucleotide frequencies are back ! These should be available eventually for all viromes (a few are still being processed). Please notify us if you encounter any unexpected behavior and/or result with these comparisons. The Metavir Team.


By sroux on 2014-08-21.
Title Nucleotide comp.
News

We are currently experiencing some trouble with the Nucleotide comparison tool. Recent projects will hence not be available to be compared from di- tri- and tetra-nucleotide frequencies. We hope to be able to fix this as soon as possible, and apologize for the incovenience. The Metavir Team.


By sroux on 2014-03-05.
Title Markers PFAM domain
News

The PFAM domain of each gene available as phylogenetic marker is now indicated on the markers table, with a link to the associated page on PFAM. Please notify us if you encounter any problem or error.


By sroux on 2013-09-10.
Title Computing outage
News

The computing cluster used by Metavir will be temporarily shut down from July 11th to 19th due to the relocation of the computing center. Hence, all currently waiting analysis are postponed to July 20th. We apologize for the inconvenience. The Metavir Team


By sroux on 2013-07-11.
Title Cluster outage
News

The computing cluster used by Metavir will be temporarily shut down in the next days for maintenance purpose. Datasets currently under analysis will thus be delayed until the cluster is available again. We apologize for this inconvenience, and try our best to set the service back to normal as soon as possible. The Metavir Team


By sroux on 2013-05-02.
Title Viral QC detection
News

Metavir is now able to detect spurious sequences which can originate from viral sequences added as quality control during high-throughput sequencing (PhiX174 and MS2 enterobacteriophages). On the taxonomy page, a warning is now displayed when several virome sequences are identical to one of these reference genomes (>98% identity). Please notify us if you encounter any unexpected behavior. The Metavir Team


By sroux on 2013-03-29.
Title Genome Cover plots
News

A new section of the contigs analysis was released, consisting of genome coverage plots based on the BLAST comparison between predicted genes from contigs and viral genomes from Refseq. These genome coverage plots can be accessed through a link at the bottom of the "Contigs maps" page. Please notify us if you encounter any unexpected behavior, or in any case of a problem. The Metavir Team


By sroux on 2013-02-07.
Title Genome Cover plots
News

A new section of the contigs analysis was released, consisting of genome coverage plots based on the BLAST comparison between predicted genes from contigs and viral genomes from Refseq. These genome coverage plots can be accessed through a link at the bottom of the "Contigs maps" page. Please notify us if you encounter any unexpected behavior, or in any case of a problem. The Metavir Team


By sroux on 2013-02-07.
Title Contigs update
News

A new version of the contigs section is now available. The major changes included in this release are a new way of loading the datasets, which should reduce the loading time especially for the contigs index, and new filters for the network (notably on BLAST scores and number of BLAST hits between two nodes). Some minor changes should also improve the general browsing experience on the website. Please notify us if there is any unexpected behavior of the site pages, or encounter any problem. The Metavir Team


By sroux on 2012-12-27.
Title Input file checks
News

New checks toward the content of input files were implemented, and can prevent some datasets to be uploaded. Metavir should now accept all fasta files (raw files, zip, or tar.gz) made of nucleotide sequences in IUPAC codes. If you encounter any trouble when trying to upload new data, please contact us. The Metavir team


By sroux on 2012-11-13.
Title New comparison tool
News

Comparison of taxonomic composition is now possible on Metavir, through a new comparison tool. This comparison is available on the "Taxonomy" page of a project, and can be viewed through Krona, or with a dynamic heatmap. We have also added a new functionality to download reads associated with recruitment plot. For each virome, you can now download all reads separated in two files : one for affiliated reads, the other for "unknown". Then, for each recruitment plot, all reads displayed or used to build the plot can be downloaded, either in one fasta file, or separated for each gene of the reference genome. All this is in Beta version right now, so please contact us if you experience any trouble or problem with this new stuff. The Metavir Team.


By sroux on 2012-10-18.
Title Database update
News

A minor change in the last Refseq update could have lead to some problem in the recruitment plot and contigs analysis with multipartite viral genomes. Metavir scripts were modified, and all projects analysed with this database were updated. Please notify us if you encounter any trouble or unexpected results. The Metavir Team.


By sroux on 2012-10-01.
Title Metavir 2 - Contigs
News

We are happy to announce the release of Metavir 2 : a new set of tools on Metavir dedicated to contigs analysis. This new part of the website aims at dealing with assembled datasets, through a new pipeline including an ORF prediction, a clustering of predicted protein in families, taxonomic compositions by gene or by contig, contig affiliation tables, contig maps, and the possibility to generate networks linking contigs and reference genomes. All these tools are still in beta version, so all inputs about bugs or suggestions for improvements will be welcomed. The Metavir Team.


By sroux on 2012-09-12.
Title Sharing projects
News

Sharing private projects between different users is now possible on Metavir. Practically, the user owning the projects (i.e. the user having uploaded it) has to go to the update project page (button "update" on the Virome Overview page), and look for users by their login or their e-mail. If the user is found, a confirmation is asked to share the project. If you encounter any trouble or weird behaviour, please contact us. The Metavir Team


By sroux on 2012-08-08.
Title Update and bug fixes
News

A new version of the recruitment plots is now available, which should be easier to read (especially the name of the different genes on the genome map). A bug was also fixed on the upload procedure, which prevented any new virome to be uploaded. Please let us know if you encounter any trouble using one of these tools (the recruitment plot and the upload). The Metavir Team


By sroux on 2012-07-24.
Title Recruitment plots
News

A new tool is available, which makes it possible to compute recruitment plots of virome reads against viral genomes in two different formats : a scatter plot with a dot for each read, or an histogram with the number of reads with a significant similarity for each genome part. These recruitment plots are based on the same BLAST comparison than the taxonomic composition. Some minor changes were also added in this release. First, we have a new way to deal with updates of the reference database : now, when a new release of Refseq is available, all taxonomic composition from public viromes are automatically updated, but the updated composition for private projects has to be manually requested on the "Taxonomy" page. Finally, the website design was slightly modified, especially the toolbar. If you experience any problem or inconvenience, please notify us. The Metavir Team


By sroux on 2012-07-11.
Title Datasets waiting
News

A great number of viromes have been submitted lately on Metavir, which means that the waiting time for any new virome will be quite long. In order for the users to estimate this waiting time, the number of datasets waiting for being processed is now displayed at the bottom on the welcome page (chart on the right), and an alert is thrown on the "upload a virome" page when more than 10 viromes are already waiting. The Metavir team.


By sroux on 2012-05-24.
Title New marker : PhoH
News

PhoH is now available as a marker gene for which phylogenetic trees can be computed. The use of this marker to assess marine phage diversity was described by Goldsmith et al.. If you encounter any trouble with the phylogenetic tree computation tool for this marker, please notify us.


By sroux on 2012-04-16.
Title New javascript trees
News

A new phylogenetic tree gallery based on jsphylosvg, a javascript plugin built to deal with tree visualization, is now available. The trees are now "dynamic" : a user can now switch between circular and linear representation, zoom in and out (in fullscreen mode), gather nodes, and access to further informations on the leaf nodes by clicking it. If you encounter any trouble with this new gallery, please notify us. Meanwhile, the former gallery is still available, by clicking the "change tree visualization" button under the tree.


By sroux on 2012-03-22.
Title Cluster outage
News

On March 6th there will be a temporary outage of the compute clusters used by Metavir, due to facilities work on the cooling systems. No new jobs will start as for this afternoon, and every currently running jobs (all phylogenetic trees computations from various users) have been stopped. These jobs, alongside new jobs which could be submitted today or tomorrow, will not be launched before Wednesday. We apologize for any inconvenience that this may cause.


By sroux on 2012-03-05.
Title New taxonomic comp.
News

Taxonomic composition are now available as raw best BLAST hit counts, in addition to the previous taxonomic composition, computed with GAAS, where BLAST hit numbers are normalized by genome length. The two compositions are displayed on the taxonomy page, and a drop-down list was added in the "computation parameters" section, to switch between these two types. If you see any surprising result, or incorrect behavior, please notify us with the contact form.


By sroux on 2012-03-01.
Title RSS Feed
News

A RSS feed is now available to follow Metavir news, with a link at the bottom of the left menu.


By sroux on 2012-03-01.
Title Non-viral datasets
News

After the question was raised in several meetings, we have decided to set up a tool to deal specifically with non-viral datasets. A pre-process is now available (as Beta version), which checks in the dataset which sequences are significantly similar to viral genomes sequences (Refseq, used for taxonomic composition), or virome sequences (Total Virome Assembly, a database we constructed and are currently annotating). Then, the metagenome is reduced to the sequences virus and / or virome-like, and all other analyses are based on this reduced dataset. The process was tested on simulated data, and seemed to work pretty well. Pre-process can be requested during the dataset upload, or can be applied to existing project via the "update" tab (on the virome overview page). We are currently ongoing tests on real datasets, so any input about this pre-process will be welcomed. Finally, as a consequence of this new kind of dataset, part of the look of the website has been modified, and any comment or bug reports would also be very useful (especially if some of the new design do not fit well with specific browsers).


By sroux on 2012-03-01.
Title Phylotree packages
News

The files downloadable on the phylogenetic tree page and the multiple-viromes phylogenetic tree page have been modified : they now include a fasta file of the nucleotidic sequences homologous to the marker (and no longer only the protein sequences). Unfortunately, these sequence will only be available for contigs (and not single reads), for the already computed trees. These files are also now distributed within a folder.


By sroux on 2011-12-19.
Title New Raref. curves
News

In order to deal with datasets with "extreme" number of sequences (either very low, less than 20 000 or very high, greater than 1 million sequences), and to correct an error in the previous way to cluster sequences, new rarefaction curves have been computed for all viromes. The results should be available within a few days. If you see anything weird (like rarefaction curves incompatible with the actual number of sequences in the dataset), and for any question, please contact the administrators.


By sroux on 2011-11-09.
Title Refseq update
News

The refseq viral genomes database, used to establish viromes taxonomic composition, has been updated to the last refseq release (2011-09-09). The taxonomic composition of previously uploaded viromes will be updated automatically. From now, this database will be automatically updated for each refseq release, and thus the taxonomic composition of viromes will hopefully be complemented with the growth of the refseq database. An additional threshold is now available for this taxonomic composition : 50 on bit-scores. This seems to be the most suitable threshold for viromes, so this is now the default one. If you see any weird thing about the taxonomic composition of your virome, or want further details, please contact us via the contact form.


By sroux on 2011-10-30.
Title New virome selection
News

A new interface is available to select viromes : they can now be gathered by project. By default, all viromes are associated with the project "Others". You can update the project of each virome on the "update" page (from Virome Overview). Please notify any bug or weird behaviour to the admins.


By sroux on 2011-10-14.
Title KRONA
News

The taxonomic composition computed by GAAS is now displayed through Krona (Sourceforge link, Pubmed link). This tool makes it possible to browse through the composition of a virome, zoom on the group(s) you are interested in, and take snapshots for publication-ready figures.
For more information, please see the Krona wiki. If you experience any trouble with the new way of displaying the taxonomic composition, please contact the administrator with the contact form.


By sroux on 2011-10-06.
Title New trees
News

Phylogenetic trees including several viromes can now be computed. Trees have to be previously computed for each virome with the marker gene. Then phylogenetic trees including the different viromes can be requested. The link for multiple-viromes trees can be found on the phylogeny page.


By sroux on 2011-09-27.
Title New marker : RdRP
News

RNA-dependant RNA polymerase (RdRP) is now available as a phylogenetic marker.


By sroux on 2011-09-23.
Title Phylogeny jobs fixed
News

We detected (and hopefully fixed) some bugs in phylogenetic jobs, which made some of them prematurely stop. We will re-run every of these jobs, so you may receive in the next days or weeks notifications about the results of an ancient job, and maybe this time there will be some phylogenetic trees generated. We are sorry for the inconvenience.


By sroux on 2011-09-22.
Title New comparison
News

Viromes can now be compared based on nucleotide composition bias (either di, tri, or tetranucleotide). This allow viromes of less than 50k sequences to be included in comparisons, conversely to the BLAST-based method. This new comparison method can be found in the "Virome comparison" tab. Any comment or bug-report will be welcomed !


By sroux on 2011-09-19.
Title MDS plot release
News

Virome comparisons are now available as MDS plots, alongside cluster trees. We are still looking for input from Metavir users, so please use the contact form for any inquiry, comment or suggestion.


By sroux on 2011-09-15.
Title Official 1.0 release
News

With the publication of the manuscript describing Metavir through Bioinformatics Advance Access, come the official 1.0 release of Metavir. We are always looking for input from Metavir users, so please use the contact form for any inquiry, comment or suggestion.


By sroux on 2011-09-13.
Title First public release
News

This is the first public release of Metavir, the web-server dedicated to virome analysis. Be aware that the paint is not quite dry, and things could not work as well as we think it should.


By sroux on 2011-03-16.
Title 0.9 Release test1
News

First release of Metavir : beta version (0.9).


By sroux on 2011-03-01.