Table 1.
Summary of twelve original genome binner and three refinning genome binner
| Genome binner | Parameters | Model | Version to validate | Publication | Last update | Resources |
|---|---|---|---|---|---|---|
| MaxBin | k-mer frequencies, coverage, single-copy genes | Expectation-maximization, bin number estimated from single-copy marker gene analysis | 2.2.6 | 2014 | 2019 | https://sourceforge.net/projects/maxbin |
| MetaBat | 4-mer frequencies, coverage | Modified K-medoids algorithm | 1&2.13 | 2015 | 2020 | https://bitbucket.org/berkeleylab/metabat/src/master |
| Groopm | coverage, contig’s length, tetranucleotide frequency | Two way clustering, Hough partitioning, self-organizing map | 2 | 2014 | 2017 | https://github.com/timbalam/GroopM |
| CONCOCT | k-mer frequencies, coverage | Gaussian mixture models, bin number determined by variable Bayesian | 1.0.0 | 2014 | 2019 | https://github.com/BinPro/CONCOCT |
| MyCC | k-mer frequencies, coverage (optional), universal single-copy genes | Affinity propagation | 1 | 2016 | 2017 | https://sourceforge.net/projects/sb2nhri |
| MetaWatt | tetranucleotide frequency, coverage | Firstly clustering by empirical relationship of the average standard deviation at tetranucleotide frequency mean, then employing interpolated Markov models | 3.5.3 | 2012 | 2016 | https://sourceforge.net/projects/metawatt |
| BMC3C | frequency variation of oligonucleotides, coverage, codon usage | Ensemble k-means, construct a weigh graph and partition it by Normalized cuts [49, 50] | \ | 2018 | 2018 | http://mlda.swu.edu.cn/codes.php?name = BMC3C |
| Binsanity | coverage, tetranucleotide frequency, percent GC content | Affinity propagation | 0.2.8 | 2017 | 2020 | https://github.com/edgraham/BinSanity |
| Autometa | sequence homology, single-copy genes, 5-mer frequency, coverage, single-copy genes | Lowest common ancestor analysis, DBSCAN algorithm, supervised decision tree classifier recruite unclustered contigs | \ | 2019 | 2020 | https://bitbucket.org/jason_c_kwan/autometa/src/master |
| COCACOLA | k-mer frequency, coverage, co-alignment, paired-end read linkage | K-means based on L1 distance, non-negative matrix factorization with sparse regularization, hierarchical clustering | \ | 2017 | 2017 | https://github.com/younglululu/COCACOLA |
| SolidBin-naive | single-copy mark genes, tetranucleotide frequencies, coverage, pairwise constraints | Semi-supervised spectral Normalized cut | 1.1 | 2019 | 2020 | https://github.com/sufforest/SolidBin |
| Vamb | tetranucleotide frequencies, coverage | Variational autoencoders, iterative medoid clustering algorithm | 2.0.1 | 2018 | 2020 | https://github.com/RasmussenLab/vamb |
| DAS Tool | original binner output bin sets | Refine bins according shared contigs between two original binner results | 1.1.1 | 2018 | 2019 | https://github.com/cmks/DAS_Tool |
| MetaWrap | original binner output bin sets | Separating every pair of contigs in different bins, selecting the best bin sets according completion and contamination | 1.2.2 | 2018 | 2019 | https://github.com/bxlab/metaWRAP |
| Binning_refiner | original binner output bin sets, single-copy genes | Scoring bins based on single-copy genes and picking up high-score bins iteratively | 1.4.0 | 2017 | 2019 | https://github.com/songweizhi/Binning_refiner |