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Table 1 Read counts per quality control step. Read counts, shown for each quality control step, are calculated taking into account forward and reverse sequences separately. MP01bCHUAC and MP03bCHUAC followed a non-enrichment method, the rest of samples followed the enrichment method. Sequencing run of each sample is also shown. Original: raw reads; Illumina QC: Typical paired-end Illumina quality control; BMTagger: Human contamination removal; Kraken2: Removal of anything except MPXV

From: A new and efficient enrichment method for metagenomic sequencing of Monkeypox virus

Sample

Run

Enriched

Original

Illumina QC

BMTagger

Kraken2

Lost reads (%)

MP01bCHUAC

A

No

7,755,402

5,897,356

306,422

179,086

97.69

MP03bCHUAC

A

No

5,204,934

4,020,926

406,616

374,718

92.80

MP01CHUAC

B

Yes

6,490,118

4,745,690

4,652,024

3,360,370

48.22

MP03CHUAC

B

Yes

5,702,680

4,030,170

4,002,176

2,695,288

52.74

MP05CHUAC

C

Yes

1,344,132

1,107,962

1,086,984

895,266

33.39

MP07CHUAC

C

Yes

1,376,066

1,111,552

1,096,070

878,534

36.16

MP08CHUAC

C

Yes

1,283,180

1,065,560

1,049,670

926,132

27.83

MP13CHUAC

C

Yes

1,576,732

1,149,468

1,025,064

631,872

59.93

MP15CHUAC

C

Yes

1,577,718

1,153,646

1,081,148

766,788

51.40

MP18CHUAC

C

Yes

1,679,854

1,136,220

1,053,980

921,610

45.14

MP19CHUAC

C

Yes

1,430,186

1,063,796

999,180

739,596

48.29

MP22CHUAC

C

Yes

1,670,392

1,317,902

1,207,964

817,532

51.06