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Benchmark against other tools #2

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tpoisot opened this issue Feb 21, 2023 · 5 comments
Open

Benchmark against other tools #2

tpoisot opened this issue Feb 21, 2023 · 5 comments

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@tpoisot
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tpoisot commented Feb 21, 2023

Benchmark elements

  • correct name
  • time
  • memory footprint

Also compare the taxo-bounded, lowercase, and fuzzy versions
@tpoisot
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tpoisot commented Feb 21, 2023 •
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Not considered for benchmark: https://www.sciencedirect.com/science/article/pii/S1673852721000837 (manual install of NCBI files + command-line tool)

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tpoisot commented Feb 21, 2023 •
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Taxopy: https://github.com/apcamargo/taxopy (requires manual file donwload but can be pointed to existing files)

Antônio Camargo, Moritz E. Beber, & Maxime Borry. (2023). apcamargo/taxopy: v0.11.0 (v0.11.0). Zenodo. https://doi.org/10.5281/zenodo.7562615

Benchmarked, speedup of NCBITaxonomy is 5x with no options, 3100x with options and taxo-bounding

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tpoisot commented Feb 21, 2023

Not considered for benchmark: https://academic.oup.com/bioinformatics/article/36/22-23/5548/6039172 - command-line only

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tpoisot commented Feb 21, 2023 •
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Not considered: taxonomizr (no mapping of names to ID, ID-centric workflow)

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tpoisot commented Feb 21, 2023

Trying to run with taxadb but it's not building on Linux

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