Biogeography: An Emerging Cornerstone for Understanding Prokaryotic Diversity, Ecology, and Evolution
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journal
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November 2006 |
Community structure and metabolism through reconstruction of microbial genomes from the environment
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journal
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February 2004 |
Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics
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journal
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November 2014 |
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
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journal
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August 2012 |
Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen
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journal
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January 2011 |
Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota
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journal
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February 2012 |
Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
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journal
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October 2013 |
Strain recovery from metagenomes
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journal
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October 2015 |
Strain-resolved community genomic analysis of gut microbial colonization in a premature infant
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journal
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December 2010 |
Niche and host-associated functional signatures of the root surface microbiome
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journal
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September 2014 |
Microbial Metagenomics: Beyond the Genome
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journal
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January 2011 |
The complete genome sequence for putative H 2 - and S-oxidizer C andidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome : Complete genome of
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journal
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April 2014 |
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw
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journal
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November 2011 |
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
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journal
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September 2012 |
Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment
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journal
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August 2013 |
Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes: Metagenomic recovery of predator prey genotypes
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journal
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July 2015 |
Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
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journal
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February 2012 |
Repetitive DNA and next-generation sequencing: computational challenges and solutions
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journal
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November 2011 |
Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut
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journal
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January 2014 |
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
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journal
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July 2012 |
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
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journal
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May 2012 |
Ray Meta: scalable de novo metagenome assembly and profiling
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journal
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January 2012 |
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
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journal
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April 2012 |
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
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journal
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January 2015 |
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs
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journal
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July 2012 |
Improved Assemblies Using a Source-Agnostic Pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of Contigs
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journal
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October 2014 |
Using cascading Bloom filters to improve the memory usage for de Brujin graphs
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journal
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January 2014 |
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
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journal
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January 2013 |
REAPR: a universal tool for genome assembly evaluation
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journal
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January 2013 |
Individual genome assembly from complex community short-read metagenomic datasets
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journal
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October 2011 |
Minimus: a fast, lightweight genome assembler
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journal
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January 2007 |
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
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journal
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February 2008 |
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
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journal
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December 2012 |
Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies
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journal
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November 2010 |
An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data
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journal
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January 2015 |
ABySS: A parallel assembler for short read sequence data
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journal
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February 2009 |
CAP3: A DNA Sequence Assembly Program
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journal
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September 1999 |
Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data
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journal
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May 2011 |
Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets
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journal
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October 2013 |
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
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journal
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April 2007 |
A General Coverage Theory for Shotgun DNA Sequencing
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journal
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July 2006 |
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
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journal
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December 2009 |
Estimating coverage in metagenomic data sets and why it matters
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journal
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May 2014 |
Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing
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journal
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November 2014 |
Ecological Succession and Viability of Human-Associated Microbiota on Restroom Surfaces
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journal
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November 2014 |
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
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journal
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May 2013 |
Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons
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journal
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December 2012 |
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
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journal
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July 2014 |
A metagenome-wide association study of gut microbiota in type 2 diabetes
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journal
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September 2012 |
Genome Project Standards in a New Era of Sequencing
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journal
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October 2009 |
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
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journal
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January 2015 |
Binning metagenomic contigs by coverage and composition
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journal
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September 2014 |
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
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journal
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October 2015 |
GroopM: an automated tool for the recovery of population genomes from related metagenomes
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journal
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January 2014 |
Alignathon: a competitive assessment of whole-genome alignment methods
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journal
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October 2014 |
GAGE: A critical evaluation of genome assemblies and assembly algorithms
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journal
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January 2012 |
Automated ensemble assembly and validation of microbial genomes
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journal
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May 2014 |
GAM-NGS: genomic assemblies merger for next generation sequencing
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journal
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April 2013 |
RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles
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journal
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January 2011 |
Applying Shannon's information theory to bacterial and phage genomes and metagenomes
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journal
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January 2013 |
Unusual biology across a group comprising more than 15% of domain Bacteria
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journal
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June 2015 |
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
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journal
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October 2013 |
Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria
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journal
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April 2015 |
A simple, fast, and accurate method of phylogenomic inference
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journal
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January 2008 |
Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2
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journal
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February 2012 |
The Pfam protein families database
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journal
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November 2011 |
The TIGRFAMs database of protein families
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journal
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January 2003 |
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage
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journal
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December 2011 |
The comprehensive microbial resource
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journal
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November 2009 |
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
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journal
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May 2015 |
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
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journal
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June 2015 |
Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data
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journal
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April 2013 |
Environmental shaping of codon usage and functional adaptation across microbial communities
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journal
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August 2013 |
Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles
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journal
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January 2011 |
Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors: Staphylococcus lugdunensis genome sequence
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journal
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July 2011 |
Sulfuricurvum kujiense gen. nov., sp. nov., a facultatively anaerobic, chemolithoautotrophic, sulfur-oxidizing bacterium isolated from an underground crude-oil storage cavity
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journal
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November 2004 |
Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance
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journal
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January 2012 |
Pvclust: an R package for assessing the uncertainty in hierarchical clustering
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journal
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April 2006 |
Community-wide analysis of microbial genome sequence signatures
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journal
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January 2009 |
Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition
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journal
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December 2011 |
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
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journal
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August 2014 |
Diversity and composition of the North Sikkim hot spring mycobiome using a culture-independent method
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journal
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March 2021 |
Automated ensemble assembly and validation of microbial genomes
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journal
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February 2014 |
Evaluation of short read metagenomic assembly
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conference
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December 2010 |
Disk Compression of k-mer Sets
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text
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January 2020 |
Biogeography: An Emerging Cornerstone for Understanding Prokaryotic Diversity, Ecology, and Evolution
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text
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January 2007 |
Using Cascading Bloom Filters to Improve the Memory Usage for de Brujin Graphs
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book
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January 2013 |
Automated ensemble assembly and validation of microbial genomes
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text
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January 2014 |
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
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preprint
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January 2014 |
Salinimonas marina sp. nov. Isolated from Jeju Island Marine Sediment
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journal
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June 2021 |
Binning Metagenomic Contigs Using Unsupervised Clustering and Reference Databases
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journal
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May 2022 |
Evaluation of short read metagenomic assembly
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journal
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January 2011 |
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs
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text
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January 2011 |
Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons
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text
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January 2012 |