Evaluation Summary


The table belows the aggregate of each assembler's evaluation across multiple genomes shown in the benchmarks. Each table entry is the coefficient of each assembler image term in a generalised linear model in the form of response ~ image + genome. The aim of this table is to provide an overview of how assemblers perform, instead of examining individual results. Each column is represented as:

  • NG50: Log-normal - larger values are better and represent an exponential larger NG50.

  • Percent Unassembled: Log-normal - smaller values are better and represent an exponentially decreasing amount of the genome left unassembled.

  • Incorrect per 100KBp: Log-normal - smaller values are better and represent an exponentially decreasing numbers of incorrect bases in the assembly.

  • Local misassemblies: Poisson - smaller values are better and represent an exponentially decreasing misassemblies.

Maintainer Image Command Bundle NG50 Percent
Unassembled
Incorrect
per 100KBp
Local
misassemblies
koadman docker-a5-miseq default 1.17 -0.56 1.39 2.25
nucleotides abyss adaptive -0.25 -0.38 2.62 0.66
nucleotides abyss default 0.11 -0.71 2.87 0.20
nucleotides abyss k-32 -1.02 -0.06 2.93 0.96
nucleotides abyss k-96 0.26 -0.51 2.57 1.06
nucleotides idba default -1.01 -0.05 0.14 -1.33
nucleotides idba idba -5.91 3.11 -1.95 -4.55
nucleotides idba single-cell -0.52 -0.06 0.29 -1.22
nucleotides megahit default -2.13 0.03 1.50 -1.16
nucleotides megahit no-mercy -1.97 0.01 1.32 -1.13
nucleotides minia careful -1.50 0.21 0.50 -1.95
nucleotides minia default -2.67 0.54 3.89 -3.86
nucleotides sga careful -0.54 0.03 0.21 -1.25
nucleotides sga default -0.29 0.10 0.25 -1.13
nucleotides soap-denovo default -2.71 0.62 -0.35 -5.24
nucleotides soap-denovo kmer-10-cutoff -2.56 0.58 -0.27 -3.63
nucleotides spades careful 0.38 -0.46 1.76 0.35
nucleotides spades default 0.34 -0.46 2.19 0.31
nucleotides spades single-cell 0.09 -0.38 2.90 0.69
nucleotides spades single-cell-careful 0.13 -0.41 1.94 0.70
nucleotides sparse-assembler careful -1.10 0.13 0.49 -1.22
nucleotides sparse-assembler default -0.99 0.08 1.01 -0.40
nucleotides velvet-optimiser default 0.05 2.10 3.98 2.25
nucleotides velvet adaptive -0.62 0.10 2.52 -2.84
nucleotides velvet careful -0.28 -0.03 0.57 -1.46
nucleotides velvet default -2.06 2.44 3.29 -18.19