RVMT enables researchers to explore a wide range of data from the global RNA virome. The user guide provides a brief overview of the data types, access methods, and
The data are available for download in several methods:
The FTP server offers the data pre-segmented at each taxonomic level. If you want to use a command line, we offer a cURL generator that will generate a command for you to execute.
Alternatively, you can retrieve the data (for all data types) directly from the NERSC FTP server from the download panel. This approach pulls a zip file containing all the data for a selected taxon. Should you need only a specific file, you can download it directly by choosing a taxon and then clicking "browse FTP".
If the FTP server is down, you can also download the data from Zenodo's permanent archive. The data set on Zenodo is not redundant and pre-segmented at each taxonomic level due to size considerations.
Within the FTP server, the data are organized in a directory structure that mirrors the taxonomy. For each taxon, there is a directory with the taxon, and within that directory, there are subdirectories for each member taxon.
➜ Norzivirales tree -L 2 ├── Atkinsviridae │ ├── Atkinsviridae_Contigs.fasta.gz │ ├── Atkinsviridae_HMMatches.tsv │ ├── Atkinsviridae_IMG_Scaffold_cart.tsv │ ├── Atkinsviridae_Info.tsv │ ├── Atkinsviridae_subtree.newick │ └── Atkinsviridae.zip ....
The following data types are included in the data set:
|Sequences||Gzipped FASTA formatted contigs|
|Metadata||Metadata for each contig, including taxonomic information|
|Annotation||Protein domain annotation for each contig, derived from hmmsearch|
|Tree||Phylogenetic tree for each taxon|
|IMG Scaffold Cart||IMG scaffold cart for each taxon|
|Zip||A compressed Zip archive with the files listed above (ZIP format).|
All taxa, as well the root, contain each of the above data types. The sole exception is that the root and any taxon that has one member do not contain a tree.
The sequences are in gzipped FASTA format.
Therefore, before using the data you need to decompress the FASTA file (unless your system has native gzip support).
To do so, you will need a tool such as
gzip or an alternative tool such as 7-zip.
Decompressing with the command line
gzip is as easy as running:
gzip will decompress the file to the same directory as the original file and then delete the compressed version.
To avoid this, you can use the
-k flag to prevent the deletion.
>ND_040544 GCTATGATGAAGCACCATTACGCTCGAATGTTGCAGATGATCACAGCCATAGGGAATATTAAAGCTTTATGTGCAATGAA TTACCCAAATCTGGATACTGTAGTCATTATAAGACGATTACTGAATGTAGCGCAATCTGTTAGTAAAATAAATCCCAGTG ... >ND_040545 ATCCTTCAACTGCTTCGGCCACAATGGCATATGAACTGTATAAGTTGTGTGATTTGGATTTTCTCAAGAAATACATAATG AAATCTCATAACACAGAACCAGCATCTATTTCTCAATCTGAGGCCTCTAGCATCCGGAAAATATTCACAGCATTCGTTTC
Each of contigs in the available FASTA files are listed as a row in the .tsv file, which contains the following metadata columns:
|String||Identifier of the data source, usually interchangeable with an IMG_Taxon_ID|
|String||Mega-Tree leaf membership|
|String||Unique contig identifier|
|Boolean||Whether the genome is segmented. Only |
|String||RdRP Identifier (if any)|
|String||A verbal description regarding abnormal contigs|
|String||The contig's genetic code|
|String||The type CRISPR which matched the contig (if any)|
|String||The lineage of the CRISPR matched spacer|
|String||The original fasta header of a contig, as it was in the original source material|
|String||The number ORFs preceded by an Shine-Delgarno RBS-like sequence|
|String||RvANI cluster membership|
|String||The affiliation level of a contig with a given tree leaf (i.e. to the value in RCR90)|
|String||The evidence for the contigs' host assignment|
|String||The host for the node|
|Integer||The length of the contig|
|String||The genome ID for the contig (only relevant for segmented genomes)|
|String||The phylum for the contig|
|String||The class for the contig|
|String||The order for the contig|
|String||The family for the contig|
|String||The genus for the contig|
|String||ITS sample ID (the unique sample identifier for a contig source)|
Source RCR90 ND Segmented RID Note Genetic_Code Type.hit Hit.s. Full_name RBS ANI90 AfLvl Host_Evidence Host Length BinID Phylum Class Order Family Genus ITS.SP.ID Novel 3300003307 Rv4_009481 ND_299653 FALSE 46525 Rv4_009481 RN90.0012994 NC98.140726 NC95_125295 NC90_009681 NC99.262892 NA Standard NA NA 3300003307_Ga0006883J46559_1007723 NA ANI90_0028208 Lvl 0 - Megatree leaves. NA NA 4553 ND_299653 4553 NA Duplornaviricota Resentoviricetes Reovirales Reoviridae NA 1031590 TRUE 3300003307 Rv4_009528 ND_299698 FALSE 46526 Rv4_009528 RN90.0013035 NC98.140769 NC95_125331 NC90_009628 NC99.262935 NA Standard NA NA 3300003307_Ga0006883J46559_1029623 NA ANI90_0028169 Lvl 0 - Megatree leaves. NA NA 3651 ND_299698 3651 NA Duplornaviricota Resentoviricetes Reovirales Reoviridae NA 1031590 TRUE 3300004477 Rv4_083540 ND_300853 FALSE 46560 Rv4_021302 NA NC98.146388 NC95_007711 NC90_039020 NC99.279419 NA Standard NA NA 3300004477_Ga0068971_1566391 NA ANI90_0019756 Lvl 2 - members of single-leaf-level ANI90 cluster NA NA 1290 ND_300853 1290 NA Duplornaviricota Resentoviricetes Reovirales Reoviridae NA 1031533 TRUE
Similarly, annotations generated by XXX are listed in a .tsv file, which contains the following metadata columns:
|String||Open reading frame identifier|
|String||Identifier of the profile (MSA or HMM) match|
|String||The start coordinate of a match on the profile|
|String||The end coordinate of a match on the profile|
|String||The matching profile length (in AA residues)|
|String||The coverage of the matching profile by the alignment|
|String||The score of the alignment|
|String||The E-value of the profile match|
|String||The contextual predicted function of the domain match|
|String||The source of the profile match|
|String||The length of the alignment of the hit to the ORF|
|String||The profile clan membership|
|String||A comment about the profile|
|String||The strand of the hit|
ND ORFID profile_accession p1 p2 pL pCoverage score evalue New_Name Analysis_Type ali_Qcov_len ClanID Comment Classified strand ND_015762 ND_015762__1__1070..1415 NVPC.4921 1 344 345 NA 291.7 1.1e-84 RdRp_bracelet-C NVPCpl 345 NA NA 1 + Duplornaviricota Resentoviricetes Reovirales Reoviridae Cypovirus_14 ND_015762 ND_015762__61138_1 EF23215.1 1 368 369 0.997289972899729 498 5.1e-148 RdRp ECOD 368 NA NA 3 + Duplornaviricota Resentoviricetes Reovirales Reoviridae Cypovirus_14 ND_015762 ND_015762__61138_1 EF24979.0 3 274 274 0.992700729927007 374.8 8.6e-111 RdRp_Reo-NTD ECOD 272 NA Reo RdRp N-terminal domain (1mukA:2-380): alpha-helical domain involved in the formation of the RNA template entry channel and access to the polymerase active site 1 + Duplornaviricota Resentoviricetes Reovirales Reoviridae Cypovirus_14
This space-separated .tsv file is able to be used to generate a IMG Scaffold Cart for the data set. For information about its format, see the IMG Scaffold Cart documentation.
Scaffold ID 3300003307 assembled Ga0006883J46559_1007723 3300003307 assembled Ga0006883J46559_1029623 3300004477 assembled Ga0068971_1566391 3300004601 assembled Ga0068934_1277308 3300004609 assembled Ga0068958_1157165
A tree is generated for each taxon using the R library castor, by prunning the megatree to tips associcated with each taxa. The trees are Newick formatted.
For simplicity sake, we have added the RdRp sequences and some of the final cluster alignments directly to our FTPs:
Another variation of the RdRps identified is available in the updated Zenodo deposit. If you have any questions, don't hesitate to contact us!
If you need help, please contact the RVMT team. You can find a contact form here or reach out directly via email at urineri (at) mail.tau.ac (dot)il. We are happy to help!
The RVMT manuscript was publised in Cell. If you use data from the RVMT, please consider citing our work with the following citation:
Neri U, Wolf YI, Roux S, Camargo AP, Lee B, Kazlauskas D, Chen IM, Ivanova N, Zeigler Allen L, Paez-Espino D, Bryant DA, Bhaya D; RNA Virus Discovery Consortium, Krupovic M, Dolja VV, Kyrpides NC, Koonin EV, Gophna U. Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell. 2022 Sep 25:S0092-8674(22)01118-7. doi:10.1016/j.cell.2022.08.023.