Tara Oceans

Tara Oceans Bacterial and Archaeal Metagenome Assembled Genomes (BAC_ARC_MAGs)
Tara Oceans Eukaryote Metagenome Assembled Genomes (SMAGs)
MetaGenomic Transcriptomes (MGT)
Tara Oceans Eukaryote Gene Catalog (MATOU) - version 1
Tara Oceans Eukaryote Gene Catalog (MATOU) - version 1.5
Single-cell genomes

Tara Oceans Bacterial and Archaeal Genomes (the "BAC_ARC_MAGs")

Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean
Tom O. Delmont, Juan Jose Pierella Karlusich, Chris Bowler, Patrick Wincker, A. Murat Eren and Eric Pelletier (2021)

Curated database of 1,888 MAGs (contig-level FASTA files): complete resource
Curated sub-database of 48 diazotrophic MAGs (contig-level FASTA files): diazotroph resource
Supplemental tables: supplemental tables
Metagenomic Co-assemblies
- Contigs >1,000nt for the 11 co-assemblies (fasta 42 Go) md5sum : 12717625b60a752d7c25ad9fb7ed1076
- Contigs >1,500nt for a targeted co-assembly of the Southern Ocean (One Giga-scale MAG) (fasta 507 Mo) md5sum : f108c1b96193563b4d39014c869eb5d6
- Contigs >2,500nt for the 11 co-assemblies (used for binning) (fasta 16 Go) md5sum : 894b7bd6700079afccf9aa038eb6c9a9
Tara Oceans Eukaryotic Genomes (the "SMAGs")

Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics
Tom O. Delmont, Morgan Gaia, Damien D. Hinsinger et. al - bioRxiv (2020)
- Curated Tara Oceans Single-Cell and Metagenome Assembled Genomes (the "SMAGs")
  - Curated database of SMAGs (contig-level FASTA files) (concatenated 6.9 Go, md5sum : 3e264c11dd3aa5d7dd2215ce61571cab / individual 6.9 Go, md5sum : f56892398915a8ea455e7cdab50d0b98)
  - 10 million protein coding genes (V.1) - beta
    - Nucleotides (concatenated 3.0 Go, md5sum : 92d68b5a6d20d2e6a60301881d2159b7 / individual 3.0 Go, md5sum : 243b0fa51b961461547a9a8508b4f9f0)
    - Peptides (concatenated 2 Go, md5sum : 0f0a635c00b98dfc4ec7e849a2670712 / individual 2.0 Go, md5sum : dd0d028f368f4454aaa1958be15be338)
    - GFF (concatenated 546 Mo, md5sum : e1511dc15a843002e7dfd6fc5457386a / individual 547 Mo, md5sum : 3b7d474185bb0cfef83cde094ceddc8e)
    - EggNog functional annotations (concatenated tab file 807 Mo, md5sum : 7dbd24c9b42a21076cbf2151698c80fc / individual tab file 807 Mo, md5sum : 7562a0bcd8288b56508b7ba4b2ee4a75)
- Metagenomic Co-assemblies
  - Contigs >1,000nt for the 11 co-assemblies (fasta 42 Go) md5sum : 12717625b60a752d7c25ad9fb7ed1076
  - Contigs >1,500nt for a targeted co-assembly of the Southern Ocean (One Giga-scale MAG) (fasta 507 Mo) md5sum : f108c1b96193563b4d39014c869eb5d6
  - Contigs >2,500nt for the 11 co-assemblies (used for binning) (fasta 16 Go) md5sum : 894b7bd6700079afccf9aa038eb6c9a9
- Curated DNA-dependent RNA polymerase
  - RNA polymerase genes in SMAGs (fasta 948 Ko) md5sum : 8a08d6a61e75bc7fb5f56dad7f17d9a8
  - RNA polymerase genes in METdb (reference transcriptomes) (fasta 844 Ko) md5sum : 96d8aba7b261b56e0bc6f1191206eda1
  - Concatenated RNA Polymerase sequences (SMAGs+metDB) (fasta 7.1 Mo) md5sum : 65ef5b41f3b86fffade28d9753abb9f4
- Other data
  - BUSCO genes raw peptides sequences (fasta 51 Mo) md5sum : 867c4e2f5ae8afbfeaddcbb367b02fba
  - Supplementary Material (pdf 4.9 Mo)
  - Supplementary Table (table 68 Mo)
  - Trees and associated metadata for the figures 1, 2 and S1 (anvio config files 688 Ko)
  - World-map projections (external link)
  MetaGenomic Transcriptomes (MGT)
  
  Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomicsMetaGenomic Transcriptomes (MGT)
  Alexey Vorobev et al. - Genome Research vol. 30 pp. 647-659 (2020)
  - Supp. Figure A1 : Taxonomic distribution of unigenes per MGT treemaps
  - Supp. Figure A2 : Geographical distribution of MGTs among Tara Ocean's samples (Biogeography maps)
  - MGT nucleic sequences (fasta file archive) [1.3 Go, md5sum : a4ce146401ef06484bec3c4e4355c076]
  - MGT abundance profile tsv fil
  - CAP3-based MGT post assemblies [1.2 Go, md5sum : 6f7cd1554a907b882097b101915ba2a8]
  - CAP3-based MGT post assemblies [1.2 Go, md5sum : 6f7cd1554a907b882097b101915ba2a8]
  - Canopy clustering source code (version d55ed1a8b825 from the original bitbucket repository)
  Tara Oceans Eukaryote Gene Catalog (the "MATOU") - version 1
  
  A global ocean atlas of eukaryotic genes
  Quentin Carradec, Eric Pelletier, et. al - Nature Communications vol.9, 373 (2018)
  - the Marine Atlas of Tara Oceans Unigenes (MATOU) Version 1 (20171115)
    - Unigene sequences (116 M) (fasta 18 Go) md5sum : a52df52fa9cda970bcc756e403f9fe51
    - Taxonomic affiliations (tab separated file) md5sum : 3d463085244df64367ad74a928814a0b
    - Proteic domains identification (tab separated file) md5sum : f22f11f2a71c824a65dd3dac8bf2d576
    - Metagenomic occurrences (tab separated file 14 Go) md5sum : 64650bf61d283178bd6772f86e503fc4
    - Metatranscriptomic occurrences (tab separated file 32 Go) md5sum : 7d2f702d1f02c7114da3ca7ad9df7574
    - Unigenes clusters composition (tab separated file 352 Mo) md5sum : f9c1a32a74c7d20f3516129d06cbb394
    - Unigenes clusters properties (tab separated file 24 Mo) md5sum : 555c1a4ddc0ac10f339eec47b89c4570
    - Reference protein database used for taxonomic affiliation (fasta file 8.1 Go) md5sum : 3adc1f95e9ef129621b1ddfd217386e7
  Tara Oceans Eukaryote Gene Catalog (the "MATOU") - version 1.5
  
  Patterns and drivers of diatom diversity and abundance in the global ocean
  Juan J. Pierella Karlusich, et al. - BioRXiv
  - the Marine Atlas of Tara Oceans Unigenes (MATOU) Version 1.5 (20171115)
    - Unigene sequences (158,348,244) (fasta 24 Go) md5sum : 045fd2cda0e99e3b6ee52b78ea572da2
    - Taxonomic affiliations (tab separated file) md5sum : 222f0e6fb9715c534e5676a432b0b444
    - Proteic domains identification (tab separated file) md5sum : 596cb13f6d196b5742babeb689a166ce
    - Metagenomic occurrences (tab separated file 9 Go) md5sum : 960dd8d864be3d661c22ec360715fc2f
    - Metatranscriptomic occurrences (tab separated file 24 Go) md5sum : 5a592d4a76eadb114a83deae7de6f71e
  Single-cell genomes
  
  Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans
  Yoann Seeleuthner, Samuel Mondy, et. al - Nature Communications vol. 9, 310 (2018)
  - MAST-3 clade A (Stramenopiles sp. TOSAG41-2)
    - co-assembly: fasta
    - gene predictions: gff3
    - predicted proteins: fasta
    - protein domains: gff3
  - MAST-3 clade F (Stramenopiles sp. TOSAG23-6)
    - co-assembly: fasta
    - gene predictions: gff3
    - predicted proteins: fasta
    - protein domains: gff3
  - MAST-4 clade A 1 (Stramenopiles sp. TOSAG23-1)
    - co-assembly: fasta
    - gene predictions: gff3
    - predicted proteins: fasta
    - protein domains: gff3
  - MAST-4 clade A 2 (Stramenopiles sp. TOSAG23-2)
    - co-assembly: fasta
    - gene predictions: gff3
    - predicted proteins: fasta
    - protein domains: gff3
  - MAST-4 clade C (Stramenopiles sp. TOSAG41-1)
    - co-assembly: fasta
    - gene predictions: gff3
    - predicted proteins: fasta
    - protein domains: gff3
  - MAST-4 clade E (Stramenopiles sp. TOSAG23-3)
    - co-assembly: fasta
    - gene predictions: gff3
    - predicted proteins: fasta
    - protein domains: gff3
  - Chrysophyte clade H 1 (Chrysophyceae sp. TOSAG23-4)
    - co-assembly: fasta
    - gene predictions: gff3
    - predicted proteins: fasta
    - protein domains: gff3
  - Chrysophyte clade H 2 (Chrysophyceae sp. TOSAG23-5)
    - co-assembly: fasta
    - gene predictions: gff3
    - predicted proteins: fasta
    - protein domains: gff3

Tara Oceans Bacterial and Archaeal Genomes (the "BAC_ARC_MAGs")

Tara Oceans Eukaryotic Genomes (the "SMAGs")

MetaGenomic Transcriptomes (MGT)

Tara Oceans Eukaryote Gene Catalog (the "MATOU") - version 1

Tara Oceans Eukaryote Gene Catalog (the "MATOU") - version 1.5

Single-cell genomes