References

Metagenomics reveals microbial diversity and metabolic potentials of seawater and surface sediment from a hadal biosphere at the yap trench

10.3389/fmicb.2018.02402 · 2018 · External reference

Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of qinhuangdao mariculture area

10.1371/journal.pone.0234128 · 2020 · External reference

A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

10.1186/s40168-018-0548-7 · 2018 · External reference

10.1093/gbe/evz184

10.1093/gbe/evz184 · External reference

10.1038/nrg3962

10.1038/nrg3962 · External reference

Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence

10.1038/s41467-019-13429-2 · 2019 · External reference

10.1371/journal.pgen.1001284

10.1371/journal.pgen.1001284 · External reference

10.1038/nrmicro2832

10.1038/nrmicro2832 · External reference

10.1038/nrg2798

10.1038/nrg2798 · External reference

Characterizing the microbiomes of antarctic sponges: a functional metagenomic approach

2020 · External reference

10.3389/fmicb.2018.03266

10.3389/fmicb.2018.03266 · External reference

Unresolved reference

External reference

10.1371/journal.pone.0218636

10.1371/journal.pone.0218636 · External reference

Characterizing the personalized microbiota dynamics for disease classification by individual-specific edge-network analysis

10.3389/fgene.2019.00283 · 2019 · External reference

Atlas: a snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

10.1186/s12859-020-03585-4 · 2020 · External reference

10.1093/nar/gkw1027

10.1093/nar/gkw1027 · External reference

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

10.1186/s40168-019-0658-x · 2019 · External reference

10.1016/j.cell.2014.12.038

10.1016/j.cell.2014.12.038 · External reference

10.1038/s41586-019-1065-y

10.1038/s41586-019-1065-y · External reference

A genome-wide association study for gut metagenome in chinese adults illuminates complex diseases

2021 · External reference

10.1038/ng.3663

10.1038/ng.3663 · External reference

10.1038/nature25973

10.1038/nature25973 · External reference

10.1038/nrmicro.2016.83

10.1038/nrmicro.2016.83 · External reference

10.1038/s41564-019-0473-y

10.1038/s41564-019-0473-y · External reference

Metagenomic data assembly–the way of decoding unknown microorganisms

10.3389/fmicb.2021.613791 · 2021 · External reference

Assembly complexity of prokaryotic genomes using short reads

10.1186/1471-2105-11-21 · 2010 · External reference

10.1089/cmb.2009.0005

10.1089/cmb.2009.0005 · External reference

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes

10.1093/bib/bbx098 · 2019 · External reference

10.1093/bioinformatics/btr520

10.1093/bioinformatics/btr520 · External reference

10.1093/bioinformatics/btt502

10.1093/bioinformatics/btt502 · External reference

Metacarvel: linking assembly graph motifs to biological variants

10.1186/s13059-019-1791-3 · 2019 · External reference

10.1038/nrmicro.2017.157

10.1038/nrmicro.2017.157 · External reference

Oral microbiome: possible harbinger for children’s health

10.1038/s41368-020-0082-x · 2020 · External reference

The microbiome of the upper respiratory tract in health and disease

10.1186/s12915-019-0703-z · 2019 · External reference

10.1111/j.1574-6941.2011.01140.x

10.1111/j.1574-6941.2011.01140.x · External reference

Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics

10.3389/fmicb.2015.00358 · 2015 · External reference

Marine microbial metagenomes sampled across space and time

10.1038/sdata.2018.176 · 2018 · External reference

10.3390/md8030608

10.3390/md8030608 · External reference

10.1101/gr.201863.115

10.1101/gr.201863.115 · External reference

10.1073/pnas.1402564111

10.1073/pnas.1402564111 · External reference

Unresolved reference

2016 · External reference

A set of measures of centrality based on betweenness

10.2307/3033543 · 1977 · External reference

10.1080/0022250x.2001.9990249

10.1080/0022250x.2001.9990249 · External reference

Stability and continuity of centrality measures in weighted graphs

2016 · External reference

Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity

10.1186/s13059-020-02066-4 · 2020 · External reference

10.1093/bioinformatics/btw312

10.1093/bioinformatics/btw312 · External reference

10.1101/gr.082784.108

10.1101/gr.082784.108 · External reference

What is the difference between the breakpoint graph and the de bruijn graph?

2014 · External reference

10.1101/gr.2395204

10.1101/gr.2395204 · External reference

Assembly of long error-prone reads using de bruijn graphs

2016 · External reference

Integrating long-range connectivity information into de bruijn graphs

10.1093/bioinformatics/bty157 · 2018 · External reference

Sigar: Inferring features of genome architecture and dna rearrangements by split-read mapping

10.1093/gbe/evaa147 · 2020 · External reference

Network structure and minimum degree

10.1016/0378-8733(83)90028-x · 1983 · External reference

Unresolved reference

External reference

Ppanggolin: depicting microbial diversity via a partitioned pangenome graph

10.1371/journal.pcbi.1007732 · 2020 · External reference

10.1101/gr.214346.116

10.1101/gr.214346.116 · External reference

10.1038/nmeth.1923

10.1038/nmeth.1923 · External reference

The igraph software package for complex network research

2006 · External reference

Openmp: An industry-standard api for shared-memory programming

1998 · External reference

10.1111/mec.12354

10.1111/mec.12354 · External reference

Unresolved reference

External reference

K-core decomposition of large networks on a single pc

10.14778/2850469.2850471 · 2015 · External reference

10.1007/s11227-009-0299-0

10.1007/s11227-009-0299-0 · External reference

Unresolved reference

2016 · External reference

wgsim-read simulator for next generation sequencing

2011 · External reference

10.1111/1462-2920.12086

10.1111/1462-2920.12086 · External reference

The human microbiome project: a community resource for the healthy human microbiome

10.1371/journal.pbio.1001377 · 2012 · External reference

Temporal and technical variability of human gut metagenomes

10.1186/s13059-015-0639-8 · 2015 · External reference

Accurate and sensitive functional screening of pathogenic sequences via ensemble learning

2021 · External reference

Unresolved reference

2019 · External reference

10.1016/j.jmoldx.2019.01.006

10.1016/j.jmoldx.2019.01.006 · External reference

10.1093/bioinformatics/btp352

10.1093/bioinformatics/btp352 · External reference

Improved metagenomic analysis with kraken 2

2019 · External reference

Probing the diversity of healthy oral microbiome with bioinformatics approaches

10.5483/bmbrep.2016.49.12.164 · 2016 · External reference

Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity

10.1186/s13059-020-02200-2 · 2020 · External reference

Comparison of subgingival and buccal mucosa microbiome in chronic and aggressive periodontitis: a pilot study

10.3389/fcimb.2019.00053 · 2019 · External reference

Impact of colonoscopy bowel preparation on intestinal microbiota

10.1371/journal.pone.0062815 · 2013 · External reference

Probiotics for the prevention of clostridium difficile-associated diarrhea in adults and children

10.1002/14651858.cd006095.pub4 · 2017 · External reference

Bacteroides fragilis prevents clostridium difficile infection in a mouse model by restoring gut barrier and microbiome regulation

10.3389/fmicb.2018.02976 · 2018 · External reference

Fecal microbiota transplant from highly feed-efficient donors shows little effect on age-related changes in feed-efficiency-associated fecal microbiota from chickens

2018 · External reference

10.3390/nu11071630

10.3390/nu11071630 · External reference

Fecal microbiota transplantation confers beneficial metabolic effects of diet and exercise on diet-induced obese mice

2018 · External reference

Identification of the microbial diversity after fecal microbiota transplantation therapy for chronic intractable constipation using 16s rrna amplicon sequencing

10.1371/journal.pone.0214085 · 2019 · External reference

The efficacy of fecal microbiota transplantation for children with tourette syndrome: A preliminary study

2020 · External reference

Separation of donor and recipient microbial diversity allows determination of taxonomic and functional features of gut microbiota restructuring following fecal transplantation

10.1128/msystems.00811-21 · 2021 · External reference

10.1136/gutjnl-2020-322630

10.1136/gutjnl-2020-322630 · External reference

The trans-kingdom battle between donor and recipient gut microbiome influences fecal microbiota transplantation outcome

2020 · External reference

Intestinal microbiome changes in fecal microbiota transplant (fmt) vs. fmt enriched with lactobacillus in the treatment of recurrent clostridioides difficile infection, Canadian

2019 · External reference

10.7554/elife.65088

10.7554/elife.65088 · External reference

10.1038/35012500

10.1038/35012500 · External reference

Gene duplication as a mechanism of genomic adaptation to a changing environment

10.1098/rspb.2012.1108 · 2012 · External reference

10.1038/nature23889

10.1038/nature23889 · External reference

MUMmer4: A fast and versatile genome alignment system

10.1371/journal.pcbi.1005944 · 2018 · External reference

Fast algorithms for determining (generalized) core groups in social networks.

10.1007/s11634-010-0079-y · 2011 · External reference