Skip to main content

Table 1 General Assembly Statistics

From: Benchmarking different approaches for Norovirus genome assembly in metagenome samples

  Sample A Sample B Sample C Sample D Sample E Sample F Sample G Sample H Average
Total number of reads 68.7 M 15.6 M 47.3 M 35.5 M 23.1 M 45.4 M 45.3 M 44.1 M 40.6 M
Ct value qRT-PCR 25.1 21.38 26.3 13.91 13.91 24.3 21.6 23.9 -
%Total NoV reads (paired, unique reads mapping norovirus) 18.5 15.6 1.4 93.9 34.4 42.9 98.6 76.5 47.7
 %Total number of reads not mapping hs37d5 60.5 80.6 76 78.2 80 66.1 68.9 71.7 72.75
Completeness YES YES YES YES YES YES YES YES -
Mean coverage depth against final contigs 453.05x 2690.55x 2587.67x 7671.9x 6309.99x 7712.23x 7805.97x 7743.57x 5371.87x
% of total reads identified by mapping (final contig) 0.026 15.79 1.43 94.31 34.32 42.97 98.77 76.93 45.57
Genotype GII.17[P17] GII.2[P2] GII.17[P17] GII.17[P17] GII.17[P17] GII.4[P4] GII.4[P31] GII.4[P4] -
Final contig length (bp) 7551 7548 7560 7594 7589 7620 7674 7634 -
Published genomes assembly strategy+ pC SPAdes pC MEGAHIT pD SPAdes pD MEGAHIT pD MEGAHIT pD MEGAHIT pD MEGAHIT pD MEGAHIT -
% identity final contig against closest RefSeq reference* 99.6 98.6 99.6 99.5 98.5 98.1 98.5 98 -
number total variants above 1 % against final genome 230 180 187 15 55 43 23 32 95.6
  1. NoV: norovirus, *closest reference norovirus genomes: -LC369255.1: samples A, C, D, E.; -MW305627.1: sample B ; -MW284782.1: samples F, H; -MW305617.1|: sample G. +(36,37) (note that these are not the best assembly strategies for each sample, more than one strategy yielded complete contigs)