metaSPAdes: a new versatile metagenomic assembler

Fast gapped-read alignment with Bowtie 2

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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

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Structure, function and diversity of the healthy human microbiome

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Cd-hit: Accelerated for clustering the next-generation sequencing data

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QUAST: quality assessment tool for genome assemblies

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Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

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MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

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Velvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint

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Enterotypes of the human gut microbiome

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The human microbiome project

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Environmental genome shotgun sequencing of the sargasso sea

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IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

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Community structure and metabolism through reconstruction of microbial genomes from the environment

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MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

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The Draft Genome of <i>Ciona intestinalis</i> : Insights into Chordate and Vertebrate Origins

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Whole-Genome Shotgun Assembly and Analysis of the Genome of <i>Fugu rubripes</i>

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A Whole-Genome Assembly of Drosophila

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Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

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Metagenomic discovery of biomass-degrading genes and genomes from cow rumen

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Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

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The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families

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MetaQUAST: evaluation of metagenome assemblies

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MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

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GAGE: A critical evaluation of genome assemblies and assembly algorithmsPreprint

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MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

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hybrid SPA des : an algorithm for hybrid assembly of short and long reads

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Gene and translation initiation site prediction in metagenomic sequences

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Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

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Prochlorococcus: the structure and function of collective diversity

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Ray Meta: scalable de novo metagenome assembly and profiling

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Community-wide analysis of microbial genome sequence signatures

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Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

Kashtan, N., Roggensack, S. E., Rodrigue, S., Berta-Thompson, J. W., Biller, S. J., Coe, A., Ding, H., Marttinen, P., Malmstrom, R. R., Stocker, R., et al. (2014) · Science · doi:10.1126/science.1248575 · Cited by 526 · see citing works

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

Dupont, C. L., Rusch, D. B., Yooseph, S., Lombardo, M., Richter, R. A., Valas, R. E., Novotny, M. A., Yee-Greenbaum, J. L., Selengut, J., Haft, D. H., et al. (2011) · The ISME Journal · doi:10.1038/ismej.2011.189 · Cited by 522 · see citing works

Sequence assembly demystified

Nagarajan, N., & Pop, M. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3367 · Cited by 474 · see citing works

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

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MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

Ashton, P., Nair, S., Dallman, T. J., Rubino, S., Rabsch, W., Mwaigwisya, S., Wain, J. R., & O’Grady, J. (2014) · Nature Biotechnology · doi:10.1038/nbt.3103 · Cited by 462 · see citing works

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

Iverson, V., Morris, R. M., Frazar, C. D., Berthiaume, C. T., Morales, R. L., & Armbrust, E. V. (2012) · Science · doi:10.1126/science.1212665 · Cited by 457 · see citing works

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

Mavromatis, K., Ivanova, N., Barry, K., Shapiro, H., Goltsman, E., McHardy, A. C., Rigoutsos, I., Salamov, A. A., Korzeniewski, F., Land, M., et al. (2007) · Nature Methods · doi:10.1038/nmeth1043 · Cited by 350 · see citing works

Meta-IDBA: a de Novo assembler for metagenomic data

Peng, Y., Leung, H. C. M., Yiu, S., & Chin, F. Y. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr216 · Cited by 326 · see citing works

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

Mende, D. R., Waller, A. S., Sunagawa, S., Järvelin, A. I., Chan, M. M., Arumugam, M., Raes, J., & Peer Bork, B. (2012) · PLoS ONE · doi:10.1371/journal.pone.0031386 · Cited by 305 · see citing works

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

Labonté, J., Swan, B. K., Poulos, B. T., Luo, H., Koren, S., Hallam, S., Sullivan, M. B., Woyke, T., Wommack, K. E., & Stepanauskas, R. (2015) · The ISME Journal · doi:10.1038/ismej.2015.48 · Cited by 241 · see citing works

De Novo Repeat Classification and Fragment AssemblyPreprint

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MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

Treangen, T. J., Koren, S., Sommer, D. D., Liu, B., Astrovskaya, I., Ondov, B., Darling, A. E., Phillippy, A. M., & Pop, M. (2013) · Genome biology · doi:10.1186/gb-2013-14-1-r2 · Cited by 225 · see citing works

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

Castelle, C., Hug, L., Wrighton, K., Thomas, B., Williams, K., Wu, D., Tringe, S., Singer, S., Eisen, J., & Banfield, J. (2013) · Nature Communications · doi:10.1038/ncomms3120 · Cited by 224 · see citing works

Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities

Shakya, M., Quince, C., Campbell, J. H., Yang, Z. K., Schadt, C. W., & Podar, M. (2013) · Environmental Microbiology · doi:10.1111/1462-2920.12086 · Cited by 215 · see citing works

Characterization of Cyanobacterial Hydrocarbon Composition and Distribution of Biosynthetic Pathways

Coates, R. C., Podell, S. B., Korobeynikov, A., Lapidus, A. L., Pevzner, P. A., Sherman, D. H., Allen, E. E., Gerwick, L. G., & Gerwick, W. H. (2014) · PLoS ONE · doi:10.1371/journal.pone.0085140 · Cited by 199 · see citing works

Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

McCoy, R. C., Taylor, R. W., Blauwkamp, T. A., Kelley, J. L., Kertesz, M., Pushkarev, D., Petrov, D. A., & Fiston-Lavier, A.-S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0106689 · Cited by 199 · see citing works

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

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Assembly of polymorphic genomes: Algorithms and application to Ciona savignyiPreprint

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A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l -tuples

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Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

McLean, J. S., Lombardo, M., Badger, J. H., Edlund, A., Novotny, M. A., Yee-Greenbaum, J. L., Vyahhi, N., Hall, A. P., Yang, Y., Dupont, C. L., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1219809110 · Cited by 171 · see citing works

Whole-genome haplotyping using long reads and statistical methods

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Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria

Kleigrewe, K., Almaliti, J., Tian, I. Y., Kinnel, R. B., Korobeynikov, A., Monroe, E. A., Duggan, B. M., Marzo, V. D., Sherman, D. H., Dorrestein, P. C., et al. (2015) · Journal of Natural Products · doi:10.1021/acs.jnatprod.5b00301 · Cited by 158 · see citing works

Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche

Rosen, M., Davison, M. R., Bhaya, D., & Fisher, D. S. (2015) · Science · doi:10.1126/science.aaa4456 · Cited by 139 · see citing works

ExSPAnder: a universal repeat resolver for DNA fragment assembly

Prjibelski, A. D., Vasilinetc, I., Bankevich, A., Gurevich, A. A., Krivosheeva, T., Nurk, S., Pham, S., Korobeynikov, A., Lapidus, A. L., & Pevzner, P. A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu266 · Cited by 138 · see citing works

Genovo: De Novo Assembly for Metagenomes

Laserson, J., Jojic, V., & Koller, D. (2011) · Journal of Computational Biology · doi:10.1089/cmb.2010.0244 · Cited by 137 · see citing works

Bambus 2: scaffolding metagenomes

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Accurate, multi-kb reads resolve complex populations and detect rare microorganismsPreprint

Sharon, I., Kertesz, M., Hug, L. A., Pushkarev, D., Blauwkamp, T. A., Castelle, C. J., Amirebrahimi, M., Thomas, B. C., Burstein, D. E., Tringe, S. G., et al. (2015) · Genome Research · doi:10.1101/gr.183012.114 · Cited by 133 · see citing works

Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome

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Omega: an Overlap-graphde novoAssembler for Metagenomics

Haider, B., Ahn, T.-H., Bushnell, B., Chai, J., Copeland, A., & Pan, C. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu395 · Cited by 96 · see citing works

Bioinformatics for the Human Microbiome Project

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Assembling short reads from jumping libraries with large insert sizes

Vasilinetc, I., Prjibelski, A. D., Gurevich, A. A., Korobeynikov, A., & Pevzner, P. A. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv337 · Cited by 79 · see citing works

Metagenomic Analysis Reveals Symbiotic Relationship among Bacteria in Microcystis-Dominated Community

Xie, M., Ren, M., Chen, Y., Yi, H., Li, Z., Li, T., & Zhao, J. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00056 · Cited by 77 · see citing works

Full Genome Virus Detection in Fecal Samples Using Sensitive Nucleic Acid Preparation, Deep Sequencing, and a Novel Iterative Sequence Classification Algorithm

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Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing

Tsai, Y., Conlan, S., Deming, C., Program, N. C. S., Segre, J. A., Kong, H. H., Korlach, J., & Oh, J. (2016) · mBio · doi:10.1128/mbio.01948-15 · Cited by 73 · see citing works

dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes

Safonova, Y., Bankevich, A., & Pevzner, P. A. (2015) · Journal of Computational Biology · doi:10.1089/cmb.2014.0153 · Cited by 70 · see citing works

Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations

García-López, R., Vázquez-Castellanos, J. F., & Moyá, A. (2015) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2015.00141 · Cited by 49 · see citing works

Spongosine Production by a Vibrio harveyi Strain Associated with the Sponge Tectitethya crypta

Bertin, M. J., Schwartz, S. L., Lee, J., Korobeynikov, A., Dorrestein, P. C., Gerwick, L. G., & Gerwick, W. H. (2015) · Journal of Natural Products · doi:10.1021/np5009762 · Cited by 42 · see citing works

TruSPAdes: barcode assembly of TruSeq synthetic long reads

Bankevich, A., & Pevzner, P. A. (2016) · Nature Methods · doi:10.1038/nmeth.3737 · Cited by 41 · see citing works

Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold

Nijkamp, J. F., Pop, M., Reinders, M. J. T., et al. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt502 · Cited by 37 · see citing works

Hapsembler: An Assembler for Highly Polymorphic Genomes

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Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome

Miller, I., Weyna, T., Fong, S., Lim-Fong, G., & Kwan, J. (2016) · Scientific Reports · doi:10.1038/srep34362 · Cited by 32 · see citing works

Using SPAdes De Novo Assembler

Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., & Korobeynikov, A. (2020) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.102 · Cited by 3,555 · see citing works

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

Uritskiy, G. V., DiRuggiero, J., & Taylor, J. (2018) · Microbiome · doi:10.1186/s40168-018-0541-1 · Cited by 2,642 · see citing works

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303 · see citing works

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

Pasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., Beghini, F., Manghi, P., Tett, A., Ghensi, P., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.001 · Cited by 1,591 · see citing works

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Blanco-Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., Manghi, P., Dubois, L., Huang, K. D., Thomas, A. M., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01688-w · Cited by 1,442 · see citing works

A unified catalog of 204,938 reference genomes from the human gut microbiome

Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0603-3 · Cited by 1,367 · see citing works

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

Ferretti, P., Pasolli, E., Tett, A., Asnicar, F., Gorfer, V., Fedi, S., Armanini, F., Truong, D. T., Manara, S., Zolfo, M., et al. (2018) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2018.06.005 · Cited by 1,292 · see citing works

A new genomic blueprint of the human gut microbiota

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Next-Generation Sequencing Technology: Current Trends and Advancements

Satam, H., Joshi, K., Mangrolia, U., Waghoo, S., Zaidi, G., Rawool, S., Thakare, R. P., Banday, S., Mishra, A. K., Das, G., et al. (2023) · Biology · doi:10.3390/biology12070997 · Cited by 1,299 · see citing works

American Gut: an Open Platform for Citizen-Science Microbiome Research

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US immigration westernizes the human gut microbiome

Vangay, P., Johnson, A. J., Ward, T. L., Al-Ghalith, G. A., Shields-Cutler, R. R., Hillmann, B. M., Lucas, S. K., Beura, L. K., Thompson, E. A., Till, L. M., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.029 · Cited by 794 · see citing works

Prevotella Diversity, Niches and Interactions with the Human Host

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The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific

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