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Table 4 Polished quality of genomes and genes

From: Promising prospects of nanopore sequencing for algal hologenomics and structural variation discovery

Assembly

Tool

% Identity

% Indels

% Substitutions

CP 1Df

Canu

96.278 (96.907)

3.615 (3.087)

0.107 (0.006)

Racon

97.418 (97.777)

2.489 (2.186)

0.093 (0.037)

Nanopolish

99.622 (99.721)

0.365 (0.265)

0.013 (0.015)

Pilon

99.929 (100.00)

0.068 (0.000)

0.003 (0.000)

CP 2D

Canu

97.951 (98.344)

2.017 (1.654)

0.032 (0.002)

Racon

98.184 (98.488)

1.785 (1.496)

0.031 (0.016)

Nanopolish

99.602 (99.707)

0.403 (0.279)

0.006 (0.015)

Pilon

99.931 (100.00)

0.066 (0.000)

0.003 (0.000)

MT 1Df

Canu

92.741 (95.767)

6.774 (4.082)

0.485 (0.158)

Racon

93.133 (95.809)

4.998 (3.131)

1.869 (1.107)

Nanopolish

98.165 (98.841)

1.190 (0.719)

0.645 (0.445)

Pilon

99.725 (99.883)

0.183 (0.056)

0.092 (0.061)

MT 2D

–

–

–

–

  1. Quality of nanopore organellar genomes and their protein-encoding genes (between parenthesis) following nanopore assembly (Canu) and polishing with successive tools (Racon, Nanopolish, and Pilon). Note the perfect accuracy of chloroplast genes following Pilon polishing. CP = Chloroplast, MT = Mitochondrion