Inference throughput (reads classified per second with four CPUs) of Kraken2 (main database, Peres da Silva et al. 2024) on ONT reads from 81 bacterial isolates (Peres da Silva et al. 2024)
13.5 Inference throughput (reads classified per second with four CPUs)
Methods
- Tested configuration
- Kraken2 (main database, Peres da Silva et al. 2024)
- Protocol
- Database storage and classification speed on ONT data, main database (Peres da Silva et al. 2024)
- Dataset
- ONT reads from 81 bacterial isolates (Peres da Silva et al. 2024)
- Procedure
- Database storage and classification speed on ONT data, main database (Peres da Silva et al. 2024)
- Evaluation
- Kraken2 on database storage and classification speed on ONT data, main database (Peres da Silva et al. 2024)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Author-reported evaluation · source checkedMetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Table 1, row "Kraken2", column "Speed (reads/sec)"
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- Not stated
- Adaptation
- All tools use the 516-genome main database
- Scoring implementation
- Speed includes database loading (Kraken2) and k-mer counting and dataset loading (MetageNN); four CPUs for all tools.
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 13.471 Individual claims | MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes Table 1, row "Kraken2", column "Speed (reads/sec)" Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | source checked ["source-hash-verification","independent-cell-check"] · 2026-10-12 author reported Audit detailsRe-downloaded the Europe PMC full-text XML and matched its SHA-256; compared the value with a separate parser of the Table 1 table-wrap and of the Results sentences written for this review. Table 1 prints 13.471 (bold as the fastest); the Results text prints 13,471 and the Discussion says MetageNN was slower than Kraken2, so the cell is a typesetting error. The cell keeps numeric_value null and the text value is the usable number. No source evidence concern: the conflict is resolved within the source and affects one speed value outside any use-case judgement. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Original source · BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML
Technical metadata and extraction receipts
Stable ID: dna-pathogen-20261012-metagenn-result-kraken2-resources-speed
- metric
- inference-throughput
- metric direction
- higher
- unit
- sample-per-second
- printed value
- 13.471
- metric qualifier
- reads classified per second with four CPUs
- source locator
- Table 1, row "Kraken2", column "Speed (reads/sec)"
- missing metadata
- uncertainty: reason: unreported
- review
- method: source-hash-verification; independent-cell-check; reviewer: claude; reviewer note: Separate Claude review agent (rev-mlvb), independent of the extracting agent; no human review claimed; date: 2026-10-12; artifact sha256: ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11022314/fullTextXML; method note: Parsed from the Table 1 <table-wrap> of the pinned XML by extract/extract_metagenn.py, with caption, header and the six method labels asserted.; note: Re-downloaded the Europe PMC full-text XML and matched its SHA-256; compared the value with a separate parser of the Table 1 table-wrap and of the Results sentences written for this review. Table 1 prints 13.471 (bold as the fastest); the Results text prints 13,471 and the Discussion says MetageNN was slower than Kraken2, so the cell is a typesetting error. The cell keeps numeric_value null and the text value is the usable number. No source evidence concern: the conflict is resolved within the source and affects one speed value outside any use-case judgement.
- numeric value
- Not reported
- unit detail
- ONT reads per second
- source discrepancy
- Table 1 prints '13.471' reads/sec, but the Results text prints 13,471 reads per second for Kraken2 and calls it the fastest tool (recorded as a separate result); numeric_value is left null.