sylph-tax - incorporating taxonomy into sylph
Note
The sylph-tax repository replaces the old sylph-utils repository. sylph-tax is easier to download/install and use than sylph-utils.
Sylph's TSV outputs do not have taxonomic information. E.g., GCA_000011.fasta is a database genome which is found within your metagenome, but this contains no information about the species, genus, order, etc.
sylph-tax can turn sylph's TSV output into a taxonomic profile like Kraken or MetaPhlAn. sylph-tax does this by using custom taxonomy files to annotate sylph's output.
Taxonomy integration - available databases with taxonomy files
The following pre-built sylph databases have available taxonomic annotations. Custom taxonomies can also be incorporated.
sylph-tax identifier (used in taxprof command) |
Database description | Clades |
|---|---|---|
| GTDB_r220 | GTDB-r220 (April 2024) | Prokaryote |
| GTDB_r214 | GTDB-r214 (April 2023) | Prokaryote |
| OceanDNA | OceanDNA - ocean MAGs from Nishimura & Yoshizawa | Prokaryote |
| SoilSMAG | Soil MAGs (SMAG) from Ma et al. | Prokaryote |
| FungiRefSeq-2024-07-25 | Refseq fungi representative genomes collected on 2024-07-25 | Eukaryote |
| TaraEukaryoticSMAG | TARA eukaryotic SMAGs from Delmont et al. | Eukaryote |
| IMGVR_4.1 | IMG/VR 4.1 high-confidence viral OTU genomes | Virus |
How do I use and install sylph-tax?
See the sylph-tax install and quick start guide here or the navigation side bar.