Profiler

Profiler

class pysylph.Profiler(database, *, minimum_ani=None, seq_id=None, estimate_unknown=False, min_number_kmers=50)

A sylph profiler.

profile(sample)

Build a taxonomic profile for the given sample.

Parameters:

sample (SampleSketch) – The sketched sample to profile.

Returns:

list of ProfileResult – The list of hits found in the database for the sample, with abundance estimates in addition to coveraged-corrected ANI.

query(sample)

Run an ANI containment query for the given sample.

Parameters:

sample (SampleSketch) – The sketched sample to profile.

Returns:

list of AniResult – The list of hits found in the database for the sample.