Hi all,
I'm working with OTU taxonomy assignments using the SILVA 138.1 database, and I'm running into issues when trying to extract the standard 7-level taxonomic hierarchy (Kingdom, Phylum, Class, Order, Family, Genus, Species).
The SILVA taxonomy strings are long and include several intermediate ranks above the Kingdom level (e.g., Eukaryota, Amorphea, Obazoa, Opisthokonta, etc.), which leads to misalignment when parsing taxonomic ranks. 📌 Example:
Here’s a sample taxonomy string assigned to a fungal OTU:
KJ720156.1.3423;Eukaryota;Amorphea;Obazoa;Opisthokonta;Nucletmycea;Fungi;Dikarya;Basidiomycota;Pucciniomycotina;Pucciniomycetes;Pucciniales;Pucciniaceae;Gymnosporangium;Gymnosporangium;ellisii
If I try to split this string by semicolons and assign standard 7 ranks, I end up with: No code has to be inserted here.Which is incorrect. The correct taxonomy should begin with Fungi as Kingdom and continue from there. 💡 Question:
How can I reliably extract just the standard 7 ranks (from Kingdom: Fungi to Species) from these extended SILVA taxonomy strings?
Are there any existing scripts/tools recommended by the SILVA community to reformat or truncate taxonomy strings to fit common microbiome analysis formats (e.g., for phyloseq in R)?
Any help or shared experience would be greatly appreciated!
Thanks,
Salma
I'm working with OTU taxonomy assignments using the SILVA 138.1 database, and I'm running into issues when trying to extract the standard 7-level taxonomic hierarchy (Kingdom, Phylum, Class, Order, Family, Genus, Species).
The SILVA taxonomy strings are long and include several intermediate ranks above the Kingdom level (e.g., Eukaryota, Amorphea, Obazoa, Opisthokonta, etc.), which leads to misalignment when parsing taxonomic ranks. 📌 Example:
Here’s a sample taxonomy string assigned to a fungal OTU:
KJ720156.1.3423;Eukaryota;Amorphea;Obazoa;Opisthokonta;Nucletmycea;Fungi;Dikarya;Basidiomycota;Pucciniomycotina;Pucciniomycetes;Pucciniales;Pucciniaceae;Gymnosporangium;Gymnosporangium;ellisii
If I try to split this string by semicolons and assign standard 7 ranks, I end up with: No code has to be inserted here.Which is incorrect. The correct taxonomy should begin with Fungi as Kingdom and continue from there. 💡 Question:
How can I reliably extract just the standard 7 ranks (from Kingdom: Fungi to Species) from these extended SILVA taxonomy strings?
Are there any existing scripts/tools recommended by the SILVA community to reformat or truncate taxonomy strings to fit common microbiome analysis formats (e.g., for phyloseq in R)?
Any help or shared experience would be greatly appreciated!
Thanks,
Salma