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Custom taxonomies

Creating custom taxonomies

If you're working with custom sylph databases, you can easily create your own taxonomy metadata file. You can look at our pre-built taxonomy files (https://zenodo.org/records/14320496) for examples.

A taxonomic metadata file is simply a two-column TSV file:

  • Column 1: the name of your genome's FASTA file:
    • my_mag.fa
  • Column 2: a semicolon-delimited taxonomy string.
    • d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A;s__Thermococcus_A alcaliphilus

Note: do not add the t__STRAIN line.

Custom taxonomy example usage case

You obtained two new MAGs: genome1.fa and genome2.fa.gz and you ran GTDB-tk to get their taxonomic annotation. You want to to profile against the new MAGs and the GTDB database.

  1. Create a file called taxonomy.tsv as follows:

    genome1.fa d__Archaea;(...);s__My new species name`
genome2.fa.gz d__Bacteria;(...);g__My genus name;s__My species name2`

  2. Use taxonomy.tsv as an argument to sylph-tax taxprof.

    ## profile against gtdb_r220 and your new MAGs
sylph profile gtdb_r220.syldb my_custom_mags.syldb ... -o gtdb+mags_output.tsv

## use your new taxonomy.tsv file and GTDB_r220
sylph-tax taxprof gtdb+mags_output.tsv -t GTDB_r220 taxonomy.tsv

Note

The parsing of the taxonomic metadata file is done in the script https://github.com/bluenote-1577/sylph-tax/blob/main/sylph_tax/sylph_to_taxprof.py. Refer to this reference implementation if needed.

Warning

Before v1.7.0 of sylph-tax, for Genbank/RefSeq genomes, filenames had to be dealt with carefully.

  • If _genomic or _ASM is in your genome file name, use the part before _genomic or _ASM.

So for GCF_002863645.1_ASM286364v1_genomic.fna.gz, use GCF_002863645.1 in column 1. This is no longer needed since v.1.7.0.

Creating taxonomy metadata from RefSeq?

See this discussion thread.