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Benchmark

M. tuberculosis read classification with standard and custom databases (Hall and Coin 2024)

Kraken and minimap2 with three databases each, scored per read on simulated and artificial real Nanopore and Illumina sputum-like metagenomes.

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Overview

Kraken and minimap2 with three databases each, scored per read on simulated and artificial real Nanopore and Illumina sputum-like metagenomes.

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Methods and evaluation design

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Baseline coverage

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Strengths, limitations and unresolved questions

Evidence

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Sources and history

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Technical metadata and extraction receipts

Stable ID: dna-pathogen-20261009-benchmark-hall2024-mtb-read-classification

areas
microbes-communities
contexts
clinical_research
entity level
suite
version
GigaScience 2024, Tables 5-8
task
Classify each non-human read as M. tuberculosis or not
source locator
Results 'Classification of Mycobacterium reads'; Methods 'Mycobacterium read classification'
scope note
Human read removal (Tables 1-4) and coverage analyses (Supplementary Tables S9-S12) are not extracted.
limitations
Read-level classification of one pathogen; not sample-level pathogen detection.
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