# TOPAZ MAGs README
Each unique TOPAZ MAG is named based on the assembly group that it was recovered from based on ocean region (OR), sample depth (D), and size fraction (SF). Finally, they are named based on their domain level classification (E for Eukaryote and P for Prokaryote). They are encoded as follows:
```
TOPAZ_[OR][D][SF]_[E]###
```
## Ocean Region
| Ocean Region | Abbreviation |
|----------------------|--------------|
| South Atlantic Ocean | SA |
| North Atlantic Ocean | NA |
| South Pacific Ocean | SP |
| North Pacific Ocean | NP |
| Indian Ocean | IO |
| Red Sea | RS |
| Mediterranean Sea | MS |
| Southern Ocean | SO |
## Saple Depth
| Depth | Abbreviation |
|-----------------------------------|--------------|
| Surface | S |
| Deep Chlorophyll Max | D |
| Mesopelagic | M |
| Filtered Seawater | F |
| Mixed surface sample (ZZZ or MIX) | X |
## Size Fraction
| Size Fraction | Abbreviation |
|---------------|--------------|
| 0.8-5 | 1 |
| 5-20 | 2 |
| 20-180 | 3 |
| 180-2000 | 4 |
# Files included for eukaryotic MAGs
For each eukaryotic MAG the following files are included:
* `TOPAZ_{*}.fna.gz`: The genomic sequence of the MAG (i.e. the binned contigs). Nucleotide fasta sequences.
* `TOPAZ_{*}.faa.gz`: The EukMetaSanity predicted proteins from the MAG. Amino acid fasta sequences.
* `TOPAZ_{*}.nr.gff3.gz`: The gff3 file used in the prediction of the amino acid sequences above.
* `TOPAZ_{*}.all.gff3.gz`: The gff3 file containing all predictions and the prediction origin (metaeuk, ab-initio, etc.).
* `mask.final.gff3.gz`: The repeat masking gff3 information from RepeatMasker.
* `mask.final.tbl`: The categories of repeats identified.
* `tax-report.txt`: The predicted taxonomy from metaeuk used in the training of gene calling.
# Files included for prokaryotic MAGs:
For each prokaryotic MAG the following files are included:
* `TOPAZ_{*}.fna.gz`: The genomic sequence of the MAG (i.e. the binned contigs). Nucleotide fasta sequences.
