Research graph
References from Unitig level assembly graph based metagenome-assembled genome refiner (UGMAGrefiner): A tool to increase completeness and resolution of metagenome-assembled genomes. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1038/nbt.3935
10.1038/nbt.3935 · External reference
Kraken: ultrafast metagenomic sequence classification using exact alignments
2014 · External reference
10.1186/s13059-019-1891-0
10.1186/s13059-019-1891-0 · External reference
Metagenome analysis using the Kraken software suite
2022 · External reference
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
2021 · External reference
Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data
10.1038/s41596-021-00508-2 · 2021 · External reference
10.1016/j.cell.2021.05.002
10.1016/j.cell.2021.05.002 · External reference
Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome
10.1038/s41467-021-21295-0 · 2021 · External reference
10.1038/s41587-020-0603-3
10.1038/s41587-020-0603-3 · External reference
Metagenomic analysis of a keratin-degrading bacterial consortium provides insight into the keratinolytic mechanisms
2021 · External reference
10.1038/s41579-020-0368-1
10.1038/s41579-020-0368-1 · External reference
10.1038/nmeth.3103
10.1038/nmeth.3103 · External reference
10.1093/bioinformatics/btv638
10.1093/bioinformatics/btv638 · External reference
10.7717/peerj.7359
10.7717/peerj.7359 · External reference
MetaDecoder: a novel method for clustering metagenomic contigs
2022 · External reference
Improved metagenome binning and assembly using deep variational autoencoders
2021 · External reference
MetaCRS: unsupervised clustering of contigs with the recursive strategy of reducing metagenomic dataset's complexity
10.1186/s12859-021-04227-z · 2022 · External reference
10.1093/bioinformatics/btz253
10.1093/bioinformatics/btz253 · External reference
vRhyme enables binning of viral genomes from metagenomes
2022 · External reference
A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments
2022 · External reference
StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities
10.1186/s13059-022-02630-0 · 2022 · External reference
Binning_refiner: improving genome bins through the combination of different binning programs
10.1093/bioinformatics/btx086 · 2017 · External reference
10.1038/s41564-018-0171-1
10.1038/s41564-018-0171-1 · External reference
10.1186/s40168-018-0541-1
10.1186/s40168-018-0541-1 · External reference
10.1016/j.ymeth.2016.02.020
10.1016/j.ymeth.2016.02.020 · External reference
10.1101/gr.213959.116
10.1101/gr.213959.116 · External reference
ORFograph: search for novel insecticidal protein genes in genomic and metagenomic assembly graphs
10.1186/s40168-021-01092-z · 2021 · External reference
GraphBin: refined binning of metagenomic contigs using assembly graphs
10.1093/bioinformatics/btaa180 · 2020 · External reference
Improving metagenomic binning results with overlapped bins using assembly graphs
10.1186/s13015-021-00185-6 · 2021 · External reference
METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs
10.1186/s12859-021-04284-4 · 2021 · External reference
Unresolved reference
2021 · External reference
Simulating Illumina metagenomic data with InSilicoSeq
10.1093/bioinformatics/bty630 · 2019 · External reference
Critical Assessment of Metagenome Interpretation: the second round of challenges
2022 · External reference
10.1093/bioinformatics/bty560
10.1093/bioinformatics/bty560 · External reference
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
2014 · External reference
10.1016/j.ebiom.2015.07.007
10.1016/j.ebiom.2015.07.007 · External reference
10.1093/bioinformatics/btu170
10.1093/bioinformatics/btu170 · External reference
10.1038/nmeth.1923
10.1038/nmeth.1923 · External reference
MUMmer4: a fast and versatile genome alignment system
10.1371/journal.pcbi.1005944 · 2018 · External reference
10.1101/gr.186072.114
10.1101/gr.186072.114 · External reference
Unresolved reference
External reference
10.1038/ismej.2017.126
10.1038/ismej.2017.126 · External reference
10.1093/bioinformatics/btu153
10.1093/bioinformatics/btu153 · External reference
Consistent metagenome-derived metrics verify and delineate bacterial species boundaries
2020 · External reference
phyloFlash: rapid small-subunit rRNA profiling and targeted assembly from metagenomes
2020 · External reference
bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes
2019 · External reference
HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps
2022 · External reference
