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 |