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.sylphmpa output format

.sylphmpa taxonomic profiling output format

*.sylphmpa files look like this: 

#SampleID       /home/jshaw/projects/temp/amr/short_reads/SRR14739086_1.fastq.gz        Taxonomies_used:['GTDB_r220']
clade_name      relative_abundance      sequence_abundance      ANI (if strain-level)    Coverage (if strain-level)
d__Bacteria     100.00010000000003      100.00019999999996      NA      NA
d__Bacteria|p__Pseudomonadota   100.00010000000003      100.00019999999996      NA      NA
d__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria    100.00010000000003      100.00019999999996      NA      NA
d__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales        35.6384 36.0603 NA      NA
....

Tip

This is a valid TSV file, but rows prefixed with # are comments. You can read .sylphmpa files with pandas in python like pd.read_csv('output.sylphmpa',sep='\t', comment='#').

Tip

You can visualize this file in pavian if you use the sylph-tax taxprof .... --pavian option (since v1.5.1).

There are five important columns:

  1. clade_name: A string like d__Bacteria|p__Actinomycetota|c__Acidimicrobiia|o__Acidimicrobiales|f__Ilumatobacteraceae that describes the clade. t__STRAIN represents the exact genome identifier.
  2. relative_abundance: the taxonomic relative abundance of the clade
  3. sequence_abundance: the sequence abundance of the clade, i.e. the % of reads assigned
  4. ANI: this is NA except for at the strain level (t__strain). Otherwise it is sylph's ANI estimate.
  5. Coverage: This is the Eff_cov or True_cov column of sylph's output.

Tip

Viral-host information may be available for pre-built virus databases. The -a option adds a new column in the .sylphmpa files associating viral genomes to their hosts. For example:

  • r__Duplodnaviria|k__Heunggongvirae|p__Uroviricota|c__Caudoviricetes|||||t__IMGVR_UViG_2503982007_000001 ... d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus;s__Staphylococcus epidermidis

indicates that IMGVR_UVIG_2503982007's host is Staphylococcus epidermidis.