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Table 1 Detailed HoCoRT performance on simulated human gut microbiome datasets

From: HoCoRT: host contamination removal tool

Pipeline

Runtime

Accuracy

Precision

Sensitivity

Paired-end HiSeq

 Seal

291.3

0.9975

0.8027

1.0000

 BBDuk

233.7

0.9952

0.6786

1.0000

 BBSplit

509.0

0.9982

0.8523

1.0000

 BioBloom

66.6

0.9990

0.9143

0.9995

 Bowtie2_end-to-end

77.4

0.9988

0.8978

1.0000

 Bowtie2_local

80.4

0.9978

0.8187

1.0000

 Bowtie2_end-to-end_un_conc

277.2

0.9934

0.9351

0.3625

 Bowtie2_local_un_conc

314.9

0.9941

0.8956

0.4614

 HISAT2

101.7

0.9990

0.9145

0.9998

 Kraken2

49.8

0.9980

0.8385

0.9928

 BBMap_default

1053.2

0.9982

0.8520

1.0000

 BBMap_fast

300.9

0.9986

0.8762

0.9999

 BWA_MEM2

381.3

0.9720

0.2635

1.0000

 Kraken2Bowtie2

87.7

0.9980

0.8385

1.0000

 Kraken2HISAT2

117.2

0.9980

0.8388

1.0000

 Minimap2_illumina

73.3

0.9977

0.8170

1.0000

 Kraken2Minimap2_illumina

105.2

0.9976

0.8107

1.0000

Paired-end MiSeq

 Seal

376.7

0.9967

0.7559

1.0000

 BBDuk

299.7

0.9916

0.5457

1.0000

 BBSplit

791.9

0.9985

0.8726

1.0000

 BioBloom

142.0

0.9990

0.9129

0.9969

 Bowtie2_end-to-end

159.0

0.9989

0.9041

0.9999

 Bowtie2_local

249.8

0.9975

0.8043

1.0000

 Bowtie2_end-to-end_un_conc

747.3

0.9904

0.9721

0.0457

 Bowtie2_local_un_conc

810.6

0.9919

0.8761

0.2243

 HISAT2

212.6

0.9990

0.9224

0.9901

 Kraken2

99.0

0.9973

0.7902

0.9960

 BBMap_default

2338.7

0.9985

0.8730

0.9993

 BBMap_fast

733.3

0.9989

0.9044

0.9956

 BWA_MEM2

2889.4

0.9128

0.1032

1.0000

 Kraken2Bowtie2

189.2

0.9973

0.7908

1.0000

 Kraken2HISAT2

236.2

0.9973

0.7908

1.0000

 Minimap2_illumina

136.5

0.9970

0.7698

1.0000

 Kraken2Minimap2_illumina

170.9

0.9967

0.7567

1.0000

Single-end Nanopore

 BioBloom

171.6

0.9900

1.0000

0.0013

 Minimap2_nanopore

179.7

0.9950

0.9965

0.5027

 Kraken2Minimap2_nanopore

256.3

0.9957

0.9632

0.5916

 Kraken2

162.4

0.9938

0.9491

0.3994

  1. The average runtime (in seconds), accuracy, precision, and sensitivity are shown for each pipeline and for each data type. The best (bold) and worst (italic) performing pipelines are indicated for each performance metric and data type
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BMC Bioinformatics

ISSN: 1471-2105

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