Table 3 Mock1 metaquast assembly report.

From: Benchmarking second and third-generation sequencing platforms for microbial metagenomics

Sequencer

Ion Proton P1 (spades)

Ion S5 (spades)

Illumina HiSeq 3000 (spades)

DNBSeq G400 (spades)

DNBSeq T7 (spades)

ONT MinION R9 (metaflye)

PacBio Sequel II (metaflye)

Nb Reads (M)

20

20

2 × 10

2 × 10

2 × 10

0.696

0.524

Nb Contigs

45,510

43,879

40,147

44,887

44,603

1,283

437

Largest Contig (bp)

384,996

794,907

1,599,668

1,063,396

1,002,925

4,324,150

7,147,004

N50 (bp)

7,847

9,089

13,707

8,519

8,184

759,940

2,013,697

Genome Fraction(%)

54.767

55.257

61.897

49.397

47.365

44.955

68.197

Mismatches per 100kbps

83.29

89.12

47.55

77.22

107.52

339.99

18.3

Indels Per 100kbps

77.8

50.03

3.53

3.23

3.67

764.45

11.76

Fully Unaligned Contigs

1,497

1,339

975

735

1,368

231

6

Fully Unaligned Length (bp)

900,150

821,545

620,805

426,856

711,992

6,279,694

134,713

NB full genome*

5

5

12

7

7

22

36

  1. Only contigs > = 500nt were aligned to the mock1 reference genomes. Number of reads, contigs and the size of the largest contig after each assembly are reported, along with: N50 (bp), a common statistic to evaluate the assembly quality; Genome fraction (%), corresponding to the mean percentage of the genome reconstructed during the assembly; the means for Mismtaches per 100kbps and Indels (Insertions/Deletions) per 100kbps, to evaluate the distance of the reconstructed genome to the reference genome). The number of fully unaligned contigs and the respective length (pb) are reported. * Full genome: More than 99% genome recovery.
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