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Merge pull request #23 from EngyNasr/reviewedFigures
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adding all tools for benchmark and updating the benchmark figure acco…
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EngyNasr authored Oct 30, 2024
2 parents 8d84413 + 87dfb30 commit 2f35ba0
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52 changes: 20 additions & 32 deletions bin/juypter_notebook_samples_without_prior_pathogen_isolation.ipynb
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84 changes: 42 additions & 42 deletions ...AIR_benchmark_Summarised_result_table.tsv → ...IR_benchmark_summarised_result _table.tsv
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Sample ID Expected Pathogen at Strain rank PathoGFAIR PathoGFAIR Comment IDseq (CZID) IDseq (CZID) Comment BugSeq
Spike1Barcode10 Salmonella enterica subsp. Enterica (DSM 554) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Above 70% identified as expected subspecies, other subspecies are also detected with minor percentages such as: enterica, houtenae indica and VII Salmonella enterica Other Salmonella species is sometimes detected in few samples: Salmonella bongori
Spike1Barcode11 Salmonella enterica subsp. Houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike1Barcode12 Salmonella enterica subsp. Salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike1Barcode13 Salmonella enterica subsp. Enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike1Barcode14 Salmonella enterica subsp. Houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike1Barcode15 Salmonella enterica subsp. Salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike2Barcode10 Salmonella enterica subsp. Enterica (DSM 554) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Salmonella enterica
Spike2Barcode11 Salmonella enterica subsp. Houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike2Barcode12 Salmonella enterica subsp. Salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike2Barcode13 Salmonella enterica subsp. Enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike2Barcode14 Salmonella enterica subsp. Houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike2Barcode15 Salmonella enterica subsp. Salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike2bBarcode10 Salmonella enterica subsp. Enterica (DSM 554) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Salmonella enterica
Spike2bBarcode11 Salmonella enterica subsp. Houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike2bBarcode12 Salmonella enterica subsp. Salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike2bBarcode13 Salmonella enterica subsp. Enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike2bBarcode14 Salmonella enterica subsp. Houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike2bBarcode15 Salmonella enterica subsp. Salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike3Barcode10 Salmonella enterica subsp. Enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike3Barcode11 Salmonella enterica subsp. Houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike3Barcode12 Salmonella enterica subsp. Salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike3Barcode13 Salmonella enterica subsp. Enterica (DSM 554) Salmonella enterica Salmonella enterica
Spike3Barcode14 Salmonella enterica subsp. Houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike3Barcode15 Salmonella enterica subsp. Salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike3bBarcode10 Salmonella enterica subsp. Enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike3bBarcode11 Salmonella enterica subsp. Houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike3bBarcode12 Salmonella enterica subsp. Salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike3bBarcode13 Salmonella enterica subsp. Enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike3bBarcode14 Salmonella enterica subsp. Houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike3bBarcode15 Salmonella enterica subsp. Salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike4Barcode01 Salmonella enterica subsp. Enterica (DSM 554) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Salmonella enterica
Spike4Barcode02 Salmonella enterica subsp. Enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike4Barcode03 Salmonella enterica subsp. Enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike4Barcode04 Salmonella enterica subsp. Enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike4Barcode05 Salmonella enterica subsp. Houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike4Barcode06 Salmonella enterica subsp. Houtenae (DSM 9221) Salmonella enterica Salmonella enterica
Spike4Barcode07 Salmonella enterica subsp. Houtenae (DSM 9221) Salmonella enterica Salmonella enterica
Spike4Barcode08 Salmonella enterica subsp. Houtenae (DSM 9221) Salmonella enterica Salmonella enterica
Spike4Barcode09 Salmonella enterica subsp. Salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike4Barcode10 Salmonella enterica subsp. Salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike4Barcode11 Salmonella enterica subsp. Salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike4Barcode12 Salmonella enterica subsp. Salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike1Barcode10 Salmonella enterica subsp. enterica (DSM 554) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Above 70% identified as expected subspecies, other subspecies are also detected with minor percentages such as: enterica, houtenae, indica and VII Salmonella enterica Other Salmonella species is sometimes detected in few samples: Salmonella bongori
Spike1Barcode11 Salmonella enterica subsp. houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike1Barcode12 Salmonella enterica subsp. salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike1Barcode13 Salmonella enterica subsp. enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike1Barcode14 Salmonella enterica subsp. houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike1Barcode15 Salmonella enterica subsp. salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike2Barcode10 Salmonella enterica subsp. enterica (DSM 554) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Salmonella enterica
Spike2Barcode11 Salmonella enterica subsp. houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike2Barcode12 Salmonella enterica subsp. salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike2Barcode13 Salmonella enterica subsp. enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike2Barcode14 Salmonella enterica subsp. houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike2Barcode15 Salmonella enterica subsp. salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike2bBarcode10 Salmonella enterica subsp. enterica (DSM 554) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Salmonella enterica
Spike2bBarcode11 Salmonella enterica subsp. houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike2bBarcode12 Salmonella enterica subsp. salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike2bBarcode13 Salmonella enterica subsp. enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike2bBarcode14 Salmonella enterica subsp. houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike2bBarcode15 Salmonella enterica subsp. salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike3Barcode10 Salmonella enterica subsp. enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike3Barcode11 Salmonella enterica subsp. houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike3Barcode12 Salmonella enterica subsp. salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike3Barcode13 Salmonella enterica subsp. enterica (DSM 554) Salmonella enterica Salmonella enterica
Spike3Barcode14 Salmonella enterica subsp. houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike3Barcode15 Salmonella enterica subsp. salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike3bBarcode10 Salmonella enterica subsp. enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike3bBarcode11 Salmonella enterica subsp. houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike3bBarcode12 Salmonella enterica subsp. salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike3bBarcode13 Salmonella enterica subsp. enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike3bBarcode14 Salmonella enterica subsp. houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike3bBarcode15 Salmonella enterica subsp. salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike4Barcode01 Salmonella enterica subsp. enterica (DSM 554) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Salmonella enterica
Spike4Barcode02 Salmonella enterica subsp. enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike4Barcode03 Salmonella enterica subsp. enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike4Barcode04 Salmonella enterica subsp. enterica (DSM 554) Salmonella enterica subsp. enterica Salmonella enterica
Spike4Barcode05 Salmonella enterica subsp. houtenae (DSM 9221) Salmonella enterica subsp houtenae Salmonella enterica
Spike4Barcode06 Salmonella enterica subsp. houtenae (DSM 9221) Salmonella enterica Salmonella enterica
Spike4Barcode07 Salmonella enterica subsp. houtenae (DSM 9221) Methylobacterium Saccharomyces cerevisiae
Spike4Barcode08 Salmonella enterica subsp. houtenae (DSM 9221) Salmonella enterica Salmonella enterica
Spike4Barcode09 Salmonella enterica subsp. salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike4Barcode10 Salmonella enterica subsp. salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike4Barcode11 Salmonella enterica subsp. salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike4Barcode12 Salmonella enterica subsp. salamae (DSM 9220) Salmonella enterica Salmonella enterica
Spike4Barcode13 1x S.Houtenea + 1x S.enterica + 10x S.Salamae Salmonella enterica subsp. enterica + Salmonella enterica subsp houtenae Salmonella enterica
Spike4Barcode14 1x S.Houtenea + 10x S.enterica + 1x S.Salamae Salmonella enterica subsp. enterica + Salmonella enterica subsp houtenae Salmonella enterica
Spike4Barcode15 10x S.Houtenea + 1x S.enterica + 1x S.Salamae Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 + Salmonella enterica subsp houtenae Salmonella enterica
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47 changes: 0 additions & 47 deletions data/benchmark/PathoGFAIR_benchmark_Results_heatmap_table.tsv
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47 changes: 47 additions & 0 deletions data/benchmark/PathoGFAIR_benchmark_results_heatmap_table.tsv
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ExpectedPathogen PathoGFAIR IDseq (CZID)
Salmonella enterica subsp. enterica (DSM 554) 4 2
Salmonella enterica subsp. houtenae (DSM 9221) 3 2
Salmonella enterica subsp. salamae (DSM 9220) 2 2
Salmonella enterica subsp. enterica (DSM 554) 3 2
Salmonella enterica subsp. houtenae (DSM 9221) 3 2
Salmonella enterica subsp. salamae (DSM 9220) 2 2
Salmonella enterica subsp. enterica (DSM 554) 4 2
Salmonella enterica subsp. houtenae (DSM 9221) 3 2
Salmonella enterica subsp. salamae (DSM 9220) 2 2
Salmonella enterica subsp. enterica (DSM 554) 3 2
Salmonella enterica subsp. houtenae (DSM 9221) 3 2
Salmonella enterica subsp. salamae (DSM 9220) 2 2
Salmonella enterica subsp. enterica (DSM 554) 4 2
Salmonella enterica subsp. houtenae (DSM 9221) 3 2
Salmonella enterica subsp. salamae (DSM 9220) 2 2
Salmonella enterica subsp. enterica (DSM 554) 3 2
Salmonella enterica subsp. houtenae (DSM 9221) 3 2
Salmonella enterica subsp. salamae (DSM 9220) 2 2
Salmonella enterica subsp. enterica (DSM 554) 3 2
Salmonella enterica subsp. houtenae (DSM 9221) 3 2
Salmonella enterica subsp. salamae (DSM 9220) 2 2
Salmonella enterica subsp. enterica (DSM 554) 2 2
Salmonella enterica subsp. houtenae (DSM 9221) 3 2
Salmonella enterica subsp. salamae (DSM 9220) 2 2
Salmonella enterica subsp. enterica (DSM 554) 3 2
Salmonella enterica subsp. houtenae (DSM 9221) 3 2
Salmonella enterica subsp. salamae (DSM 9220) 2 2
Salmonella enterica subsp. enterica (DSM 554) 3 2
Salmonella enterica subsp. houtenae (DSM 9221) 3 2
Salmonella enterica subsp. salamae (DSM 9220) 2 2
Salmonella enterica subsp. enterica (DSM 554) 4 2
Salmonella enterica subsp. enterica (DSM 554) 3 2
Salmonella enterica subsp. enterica (DSM 554) 3 2
Salmonella enterica subsp. enterica (DSM 554) 3 2
Salmonella enterica subsp. houtenae (DSM 9221) 3 2
Salmonella enterica subsp. houtenae (DSM 9221) 2 2
Salmonella enterica subsp. houtenae (DSM 9221) 0 0
Salmonella enterica subsp. houtenae (DSM 9221) 2 2
Salmonella enterica subsp. salamae (DSM 9220) 2 2
Salmonella enterica subsp. salamae (DSM 9220) 2 2
Salmonella enterica subsp. salamae (DSM 9220) 2 2
Salmonella enterica subsp. salamae (DSM 9220) 2 2
1x S.Houtenea + 1x S.enterica + 10x S.Salamae 3 2
1x S.Houtenea + 10x S.enterica + 1x S.Salamae 3 2
10x S.Houtenea + 1x S.enterica + 1x S.Salamae 4 2
5x S.Houtenea + 5x S.enterica + 5x S.Salamae 4 2
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