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Subcommand information

download - download taxonomy metadata

sylph-tax download --download-to /my/folder/sylph_taxonomy_files/
  • Downloads taxonomic annotation files (~50 MB; see here) to --download-to.
  • The --download-to folder must exist. The location can be wherever. Its location is written to ~/.config/sylph-tax/config.json.
  • If you don't have access to $HOME, you can specify a custom location in the SYLPH_TAXONOMY_CONFIG environment variable. E.g. export SYLPH_TAXONOMY_CONFIG=/write_access_folder/sylph-tax-config.json.

taxprof - taxonomic profiles from sylph's output

sylph-tax taxprof sylph_results/*.tsv  -o prefix_or_folder/ -t {sylph-tax identifier}
  • sylph_results/*.tsv: outputs from sylph. The databases used for sylph must be the same as the -t option.
  • -t/--taxonomy-metadata: A list of sylph-tax identifiers specified in this table (e.g. GTDB_r220 or IMGVR_4.1). Multiple taxonomy metadata files can be input. Custom taxonomy files are also possible.
  • -o: prepends this prefix to all of the output files. One file is output per sample in sylph_output.tsv
  • -a/--annotate-virus-hosts: annotates viral genomes with host information metadata (only works if using a pre-built viral database)
  • --pavian: outputs a taxonomy file that can be visualized via pavian but removes some relevant statistics.
  • Output suffix is .sylphmpa.

Tip

In python/pandas, pd.read_csv('output.sylphmpa',sep='\t', comment='#') works.

merge - merge multiple taxonomic profiles

sylph-tax merge *.sylphmpa --column {ANI, relative_abundance, sequence_abundance} -o output_table.tsv
  • *.sylphmpa files are outputs from sylph-tax taxprof.
  • --column can be ANI, relative abundance, or sequence abundance (see paper for difference between abundances)
  • -o output file in TSV format.

Output format for merge (TSV)

clade_name  sample1.fastq.gz  sample2.fastq.gz
d__Archaea  0.0  1.1
d__Archaea|p__Methanobacteriota 0.0     0.0965
...