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* The Ocean Microbial Reference Gene Catalog v2 (OM-RGC.v2)                          *
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Last change: 07.March.2019

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* Files                                                                              *
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Existing files:

Gene catalog:
    OM-RGC_v2_release.tsv.gz
    OM-RGC_v2_genes.fna
    OM-RGC_v2_assemblies.tar.gz

Gene profiles:
    OM-RGC_v2_gene_profile_metaG.tsv.gz
    OM-RGC_v2_gene_profile_metaT.tsv.gz

Functional profiles:
  OM-RGC_v2_functional_profile_KEGG.tar.gz
    KO_exp.norm.match.log2.tsv.gz
    KO_metaG.norm.match.log2.tsv.gz
    KO_metaG.norm.tsv.gz
    KO_metaT.norm.match.log2.tsv.gz
    KO_metaT.norm.tsv.gz
  OM-RGC_v2_functional_profile_eggNOG.tar.gz
    OG_exp.norm.match.log2.tsv.gz
    OG_metaG.norm.match.log2.tsv.gz
    OG_metaG.norm.tsv.gz
    OG_metaT.norm.match.log2.tsv.gz
    OG_metaT.norm.tsv.gz
  OM-RGC_v2_functional_profile_eggNOGplusGC.tar.gz
    OGplusGC_exp.norm.match.log2.tsv.gz
    OGplusGC_metaG.norm.match.log2.tsv.gz
    OGplusGC_metaG.norm.tsv.gz
    OGplusGC_metaT.norm.match.log2.tsv.gz
    OGplusGC_metaT.norm.tsv.gz

Taxonomic profiles:
  OM-RGC_v2_taxonomic_profiles.tar.gz
    mitags_tab_class.tsv.gz
    mitags_tab_domain.tsv.gz
    mitags_tab_family.tsv.gz
    mitags_tab_genus.tsv.gz
    mitags_tab_order.tsv.gz
    mitags_tab_otu.tsv.gz
    mitags_tab_phylum.tsv.gz

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* File description                                                                   *
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Field separator for all files is a single '\t' character.

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Gene catalog:
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The file OM-RGC_v2_release.tsv.gz contains all reference genes in a single .tsv file
for easy insertion into databases.
Each row contains the following information:

1. gene      Gene identifier (with link to scaffold origin)
2. OM-RGC_ID Internal identifier of the sequence (OM-RGC.v2.XXXXXXXXX)
3. KO        KEGG annotated KEGG orthology of this gene (if available)
4. OG        eggNOG annotated orthologous group(s) of this gene (if available)
5. GC        gene cluster representative ID (if available)
6. Domain    Taxonomic annotation (Domain)
7. Phylum    Taxonomic annotation (Phylum)
8. Class     Taxonomic annotation (Class)
9. Order     Taxonomic annotation (Order)
10. Family   Taxonomic annotation (Family)
11. Genus    Taxonomic annotation (Genus)
12. Species  Taxonomic annotation (Species)
13. Strain   Taxonomic annotation (Strain)
14. sequence Nucleotide sequence of the gene

The file OM-RGC_v2_genes.fna contains all gene sequences in FASTA format.
The file OM-RGC_v2_assemblies.tar.gz contains one file for each sample with all  assemblies in FASTA format.

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Gene profiles:
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Contain the composition (length–normalized insert counts) for each gene in
the 180 metagenomic samples [gene_profile_metaG.tsv.gz] and the 187
metatranscriptomic samples [gene_profile_metaT.tsv.gz].

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Functional profiles:
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Contain the genomic and transcriptomic composition and expression for each
OG/KO/GC in each sample.

Profiles are built for three different metric:
  - genomic composition [*metaG*.tsv.gz]
  - transcriptomic composition [*metaT*.tsv.gz]
  - expression levels (transcriptomic composition/genomic composition) [*exp*.tsv.gz]

Profiles are built for three different functional annotations:
  - KOs [KO_*.tsv.gz]
  - OGs [KO_*.tsv.gz]
  - OGs+GC [OGplusGC_*.tsv.gz]

Profiles with two different normalization are shared (see details in STAR Methods):
  - per-cell abundance [*norm*.tsv.gz]
  - per-cell abundance + Variance stabilization + log2 [*norm.match.log2.tsv.gz]

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Taxonomic profiles:
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Contain the composition (number of 16S/18S metagenomic reads) of each taxa
(and the unclassified reads) in each sample. Composition tables exist for 7 different
taxonomic levels (Domain, Phylum, Class, Order, Family, Genus, 97% OTUs).


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* Disclaimer                                                                         *
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The data have been generated according to current standards of scientific conduct.
However, gene coding nucleotide sequences represent computational predictions only
and accuracy of taxonomic and gene functional assignments dependent on the completeness
of reference databases used for annotation. Thus, the data provider cannot be held
responsible for potential mispredictions or misannotations.