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Table 2 Overview of taxonomic profiling methods used in this experiment

From: Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

Intended Use

Method

Variations

Reference database

Strategy

Short reads

Kraken2

“PlusPF”

K-mer-based

Bracken

“PlusPF”

Bayesian Refinement

Centrifuge

h22, h500

Refseq ABVF

BW transform, FM-index

MetaPhlAn3

mpa_v30_CHOCOPhlAn_201901

Read mapping, coverage scores

mOTUs2

V3.0.3

Read mapping

General

sourmash

k31, k51

GenBank

K-mer min-set-cov; LCA algorithm

Long reads

MetaMaps

MiniSeq + H

Approximate mapping

MMseqs2

NCBI nr

Translation alignment, LCA algorithm

MEGAN-LR-prot

NCBI nr

Translation alignment, LCA algorithm

MEGAN-LR-nuc

HiFi, ONT

NCBI nt

Nucleotide alignment, LCA algorithm

BugSeq-V2

NCBI nt

Nucleotide alignment, LCA algorithm