Cited by 2,132Genomics and Phylogenetic StudiesAlgorithms and Data CompressionMicrobial Community Ecology and Physiology

The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.

PANDAseq: paired-end assembler for illumina sequences

Open access

Masella, Andre P, Bartram, Andrea K, Truszkowski, Jakub M, Brown, Daniel G, Neufeld, Josh D·2012·BMC Bioinformatics

DOI 10.1186/1471-2105-13-31PMC PMC3471323

Open this paper in CoChat — free account Open PDF

Abstract

BACKGROUND: Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence yields using quality information. RESULTS: PANDAseq assembles paired-end reads rapidly and with the correction of most errors. Uncertain error corrections come from reads with many low-quality bases identified by upstream processing. Benchmarks were done using real error masks on simulated data, a pure source template, and a pooled template of genomic DNA from known organisms. PANDAseq assembled reads more rapidly and with reduced error incorporation compared to alternative methods. CONCLUSIONS: PANDAseq rapidly assembles sequences and scales to billions of paired-end reads. Assembly of control libraries showed a 4-50% increase in the number of assembled sequences over naïve assembly with negligible loss of "good" sequence.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1186/1471-2105-13-31

Cites

12 of 12 references verified0 citation errors · 0 not checkable

Statistics

Figure 1 Schematic of paired-end assembly. Typical scenario: forward and reverse reads are overlapped and the primer regions are removed to reconstruct the sequences. Highly overlapping scenario: for short templates, the overlapping region may include the primer regions.CC BY · PubMed Central

Figure 2 Quality scores of assembled masked data. A perfect 16S rRNA sequence from Sinorhizobium meliloti was masked using real Illumina quality scores and the resulting paired-end sequences were assembled with PANDAseq. A histogram of quality scores for the assembled sequences is shown.CC BY · PubMed Central

Figure 3 Comparison of output of various assemblers. A scatter plot of the percentage of paired-end sequence assemblies from sequenced V3-region amplicons of Methylococcus capsulatus strain Bath against the average number of mismatching nucleotides between the assembled sequence and the reference sequence. The comparison was done between PANDAseq and three alternative assemblers (see text).CC BY · PubMed Central

Figure 4 Rank abundance curves for control libraries. Rank-abundance curves for defined multi-organism libraries [1] assembled at two different quality thresholds using PANDAseq and naïve assembly followed by clustering with CD-HIT into OTUs of 97% identity.CC BY · PubMed Central

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
Muyzer, G., de Waal, E. C., & Uitterlinden, A. G. (1993) · Applied and Environmental Microbiology · doi:10.1128/aem.59.3.695-700.1993 · Cited by 11,490
A general method applicable to the search for similarities in the amino acid sequence of two proteins
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Li, W.-Z., & Godzik, A. (2006) · Bioinform. · doi:10.1093/bioinformatics/btl158 · Cited by 10,996
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C., Turnbaugh, P. J., Fierer, N., & Knight, R. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000080107 · Cited by 9,944
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T. L., Garrity, G. M., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn879 · Cited by 4,873
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
Cock, P., Fields, C. J., Goto, N., Heuer, M., & Rice, P. M. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1137 · Cited by 1,896
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
Cole, J. R., Chai, B., Farris, R. J., Wang, Q., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Bandela, A. M., Cardenas, E., Garrity, G. M., & Tiedje, J. M. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl889 · Cited by 1,171
Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads
Bartram, A. K., Lynch, M. D. J., Stearns, J. C., Moreno‐Hagelsieb, G., & Neufeld, J. D. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.02772-10 · Cited by 800
Self-citation
Illumina-based analysis of microbial community diversity
Degnan, P. H., & Ochman, H. (2011) · The ISME Journal · doi:10.1038/ismej.2011.74 · Cited by 422
Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products
Gloor, G. B., Hummelen, R., Macklaim, J. M., Dickson, R. J., Fernandes, A. D., MacPhee, R., & Reid, G. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015406 · Cited by 330

Show all 12 references

Research works printed but not linked: 1

Illumina, Inc: CASAVA Software Version 1.7 User Guide. Illumina, Inc; 2010.

Sorted by citations

Items 701–800 of 1,002

PCR Primers to Study the Diversity of Expressed Fungal Genes Encoding Lignocellulolytic Enzymes in Soils Using High-Throughput Sequencing
Barbi, F., Bragalini, C., Vallon, L., Prudent, E., Dubost, A., Fraissinet‐Tachet, L., Marmeisse, R., & Luis, P. (2014) · PLoS ONE · doi:10.1371/journal.pone.0116264 · Cited by 41
Early modifications of the gut microbiome in children with hepatic sinusoidal obstruction syndrome after hematopoietic stem cell transplantation
Masetti, R., Biagi, E., Zama, D., Muratore, E., D’Amico, F., Leardini, D., Turroni, S., Prete, A., Brigidi, P., & Pession, A. (2021) · Scientific Reports · doi:10.1038/s41598-021-93571-4 · Cited by 41
Gentamicin at sub-inhibitory concentrations selects for antibiotic resistance in the environment
Sanchez-Cid, C., Guironnet, A., Keuschnig, C., Wiest, L., Vulliet, E., & Vogel, T. M. (2022) · ISME Communications · doi:10.1038/s43705-022-00101-y · Cited by 40
A population modification gene drive targeting both Saglin and Lipophorin impairs Plasmodium transmission in Anopheles mosquitoes
Green, E. I., Jaouen, E., Klug, D., Olmo, R. P., Gautier, A., Blandin, S. A., & Marois, É. (2023) · eLife · doi:10.7554/elife.93142 · Cited by 42
Molecular characterization of canine kobuvirus in wild carnivores and the domestic dog in Africa.
Olarte‐Castillo, X. A., Heeger, F., Mazzoni, C., Greenwood, A., Fyumagwa, R., Moehlman, P., Hofer, H., & East, M. (2015) · Virology · doi:10.1016/j.virol.2015.01.010 · Cited by 41
False positives complicate ancient pathogen identifications using high-throughput shotgun sequencing
Campana, M. G., García, N. M. R., Rühli, F. J., & Tuross, N. (2014) · BMC Research Notes · doi:10.1186/1756-0500-7-111 · Cited by 44
Experimental Climate Change Modifies Degradative Succession in Boreal Peatland Fungal Communities
Asemaninejad, A., Thorn, R. G., & Lindo, Z. (2016) · Microbial Ecology · doi:10.1007/s00248-016-0875-9 · Cited by 40
Variations in diet cause alterations in microbiota and metabolites that follow changes in disease severity in a multiple sclerosis model
Libbey, J. E., Sanchez, J. M. S., Doty, D. J., Sim, J. T., Cusick, M. F., Cox, J. E., Fischer, K. F., Round, J. L., & Fujinami, R. S. (2018) · Beneficial Microbes · doi:10.3920/bm2017.0116 · Cited by 40
Spatial patterns of pathogenic and mutualistic fungi across the elevational range of a host plant
Merges, D., Bálint, M., Schmitt, I., Böhning‐Gaese, K., & Neuschulz, E. L. (2018) · Journal of Ecology · doi:10.1111/1365-2745.12942 · Cited by 42
Response of bentonite microbial communities to stresses relevant to geodisposal of radioactive waste
Haynes, H. M., Pearce, C. I., Boothman, C., & Lloyd, J. R. (2018) · Chemical Geology · doi:10.1016/j.chemgeo.2018.10.004 · Cited by 40
Classification of individuals and the potential to detect sexual contact using the microbiome of the pubic region
Williams, D. W., & Gibson, G. C. (2019) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2019.05.004 · Cited by 40
Neonatal Exposure to Amoxicillin Alters Long-Term Immune Response Despite Transient Effects on Gut-Microbiota in Piglets
Fouhse, J. M., Yang, K., Juan More, B., Gao, Y., Goruk, S., Plastow, G. S., Field, C. J., Barreda, D. R., & Willing, B. P. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.02059 · Cited by 40
The Compositionally Distinct Cyanobacterial Biocrusts From Brazilian Savanna and Their Environmental Drivers of Community Diversity
de Lima, N. M., Fernandes, V., Roush, D., Ayuso, S. V., Rigonato, J., García‐Pichel, F., & Branco, L. H. Z. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02798 · Cited by 40
The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes
Verbanic, S., Deacon, J. M., & Chen, I. A. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.02777-21 · Cited by 39
Dietary glycerol monolaurate improved the growth, activity of digestive enzymes and gut microbiota in zebrafish (Danio rerio)
Wang, Y., Abdullah, Zhong, H., Wang, J., & Feng, F. (2021) · Aquaculture Reports · doi:10.1016/j.aqrep.2021.100670 · Cited by 39
Light attenuation in enriched purple phototrophic bacteria cultures: Implications for modelling and reactor design
Capson‐Tojo, G., Batstone, D. J., Grassino, M., & Hülsen, T. (2022) · Water Research · doi:10.1016/j.watres.2022.118572 · Cited by 39
Microbial Community Analysis by Single-Amplicon High-Throughput Next Generation Sequencing: Data Analysis – From Raw Output to Ecology
Dumbrell, A. J., Ferguson, R., & Clark, D. R. (2016) · Springer protocols handbooks/Springer protocols · doi:10.1007/8623_2016_228 · Cited by 41
Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens
Chopyk, J., Chattopadhyay, S., Kulkarni, P., Claye, E., Babik, K. R., Reid, M. C., Smyth, E. M., Hittle, L. E., Paulson, J. N., Cruz‐Cano, R., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0235-0 · Cited by 42
TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome
Stedtfeld, R. D., Stedtfeld, T. M., Fader, K. A., Williams, M. R., Bhaduri, P., Quensen, J. F., Zacharewski, T. R., Tiedje, J. M., & Hashsham, S. A. (2017) · FEMS Microbiology Ecology · doi:10.1093/femsec/fix058 · Cited by 40
Metatranscriptomics reveals the hydrolytic potential of peat-inhabiting Planctomycetes
Ivanova, A. A., Wegner, C., Kim, Y., Liesack, W., & Dedysh, S. N. (2017) · Antonie van Leeuwenhoek · doi:10.1007/s10482-017-0973-9 · Cited by 39
Dietary supplementation of weaned piglets with a yeast-derived mannan-rich fraction modulates cecal microbial profiles, jejunal morphology and gene expression
Fouhse, J. M., Dawson, K. A., Graugnard, D. E., Dyck, M. K., & Willing, B. P. (2019) · animal · doi:10.1017/s1751731118003361 · Cited by 39
Hydrogen production in reactors: The influence of organic loading rate, inoculum and support material
Vilela, R. S., Saia, F. T., Gregoracci, G. B., Duarte, R. T. D., de Andrade, P. A. M., van der Zaan, B., Langenhoff, A. A. M., & Damianovic, M. H. R. Z. (2019) · International Journal of Hydrogen Energy · doi:10.1016/j.ijhydene.2019.08.180 · Cited by 39
Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient
Seward, J., Carson, M. A., Lamit, L. J., Basiliko, N., Yavitt, J. B., Lilleskov, E. A., Schadt, C. W., Smith, D. S., Mclaughlin, J. W., Mykytczuk, N., et al. (2020) · Microbial Ecology · doi:10.1007/s00248-020-01510-z · Cited by 40
Effect of Chlorination on Microbiological Quality of Effluent of a Full-Scale Wastewater Treatment Plant
Zerva, I., Remmas, N., Kagalou, I., Melidis, P., Ariantsi, M., Sylaios, G. K., & Ntougias, S. (2021) · Life · doi:10.3390/life11010068 · Cited by 39
Extensive Overlap of Tropical Rainforest Bacterial Endophytes between Soil, Plant Parts, and Plant Species
Haruna, E., Zin, N. M., Kerfahi, D., & Adams, J. M. (2017) · Microbial Ecology · doi:10.1007/s00248-017-1002-2 · Cited by 43
Comparative analyses of the gut microbiota among three different wild geese species in the genus Anser
Wang, W., Liu, Y., Yang, Y., Wang, A., Sharshov, K., Li, Y., Cao, M., Mao, P., & Li, L. (2018) · Journal of Basic Microbiology · doi:10.1002/jobm.201800060 · Cited by 37
Assessment of insert sizes and adapter content in fastq data from NexteraXT libraries
Turner (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00005 · Cited by 38
Vertical stratification of the foliar fungal community in the world's tallest trees
Harrison, J. G., Forister, M. L., Parchman, T. L., & Koch, G. W. (2016) · American Journal of Botany · doi:10.3732/ajb.1600277 · Cited by 38
Bacterial community structure and prevalence of Pusillimonas-like bacteria in aged landfill leachate
Remmas, N., Roukouni, C., & Ntougias, S. (2017) · Environmental Science and Pollution Research · doi:10.1007/s11356-017-8416-8 · Cited by 38
Patterns and drivers of fungal community depth stratification in Sphagnum peat
Lamit, L. J., Romanowicz, K. J., Potvin, L. R., Rivers, A. R., Singh, K. P., Lennon, J. T., Tringe, S. G., Kane, E. S., & Lilleskov, E. A. (2017) · FEMS Microbiology Ecology · doi:10.1093/femsec/fix082 · Cited by 38
Cutaneous Microbial Community Variation across Populations of Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis)
Hernández‐Gómez, O., Hoverman, J. T., & Williams, R. N. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01379 · Cited by 39
Dietary supplementation with flaxseed meal and oat hulls modulates intestinal histomorphometric characteristics, digesta- and mucosa-associated microbiota in pigs
Ndou, S. P., Tun, H. M., Kiarie, E. G., Walsh, M. C., Khafipour, E., & Nyachoti, C. M. (2018) · Scientific Reports · doi:10.1038/s41598-018-24043-5 · Cited by 38
Bacterial Response to Permafrost Derived Organic Matter Input in an Arctic Fjord
Müller, O., Seuthe, L., Bratbak, G., & Paulsen, M. L. (2018) · Frontiers in Marine Science · doi:10.3389/fmars.2018.00263 · Cited by 38
Anadromous Arctic Char Microbiomes: Bioprospecting in the High Arctic
Hamilton, E. F., Element, G., de Groot, P. V. C., Engel, K., Neufeld, J. D., Shah, V., & Walker, V. K. (2019) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2019.00032 · Cited by 40
Self-citation
Impacts of long‐term elevated atmospheric CO2 concentrations on communities of arbuscular mycorrhizal fungi
Maček, I., Clark, D. R., Šibanc, N., Moser, G. M., Vodnik, D., Müller, C., & Dumbrell, A. J. (2019) · Molecular Ecology · doi:10.1111/mec.15160 · Cited by 44
Effects of an over-the-counter lactic-acid containing intra-vaginal douching product on the vaginal microbiota
van der Veer, C., Bruisten, S. M., van Houdt, R., Matser, A. A., Tachedjian, G., van de Wijgert, J. H. H. M., de Vries, H. J. C., & van der Helm, J. J. (2019) · BMC Microbiology · doi:10.1186/s12866-019-1545-0 · Cited by 41
Ecological Differentiation in Two Major Freshwater Bacterial Taxa Along Environmental Gradients
Nuy, J. K., Hoetzinger, M., Hahn, M. W., Beißer, D., & Boenigk, J. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00154 · Cited by 38
Testing the Two-Step Model of Plant Root Microbiome Acquisition Under Multiple Plant Species and Soil Sources
Barajas, H. R., Martínez-Sánchez, S., Romero, M. F., Hernández-Álvarez, C., Servín‐González, L., Peimbert, M., Cruz‐Ortega, R., García‐Oliva, F., & Alcaraz, L. D. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.542742 · Cited by 42
Accumulation of detached kelp biomass in a subtidal temperate coastal ecosystem induces succession of epiphytic and sediment bacterial communities
Brunet, M., de Bettignies, F., Duff, N. L., Tanguy, G., Davoult, D., Leblanc, C., Gobet, A., & Thomas, F. (2021) · Environmental Microbiology · doi:10.1111/1462-2920.15389 · Cited by 38
Tree species select diverse soil fungal communities expressing different sets of lignocellulolytic enzyme-encoding genes
Barbi, F., Prudent, E., Vallon, L., Buée, M., Dubost, A., Legout, A., Marmeisse, R., Fraissinet‐Tachet, L., & Luis, P. (2016) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2016.06.008 · Cited by 38
Effects of organic loading rates on microbial communities and biogas production from water hyacinth: a case of mono‐ and co‐digestion
Nkuna, R., Roopnarain, A., & Adeleke, R. A. (2018) · Journal of Chemical Technology & Biotechnology · doi:10.1002/jctb.5886 · Cited by 38
Can We Estimate Functionality of Soil Microbial Communities from Structure-Derived Predictions? A Reality Test in Agricultural Soils
Breitkreuz, C., Heintz‐Buschart, A., Buscot, F., Wahdan, S. F. M., Tarkka, M. T., & Reitz, T. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.00278-21 · Cited by 42
Plant enhancers exhibit both cooperative and additive interactions among their functional elements
Jores, T., Tonnies, J., Mueth, N. A., Romanowski, A., Fields, S., Cuperus, J. T., & Queitsch, C. (2024) · The Plant Cell · doi:10.1093/plcell/koae088 · Cited by 37
Diversity of Bacterial Communities on Four Frequently Used Surfaces in a Large Brazilian Teaching Hospital
da Fonseca, T. A. P., Pessôa, R., Félix, A. C., & Sanabani, S. S. (2016) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph13020152 · Cited by 37
Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s “species minimum” concept
Pavloudi, C., Oulas, A., Kristoffersen, J. B., Friedrich, M. W., & Arvanitidis, C. (2017) · PeerJ · doi:10.7717/peerj.3687 · Cited by 37
Targeted Diet Modification Reduces Multiple Sclerosis–like Disease in Adult Marmoset Monkeys from an Outbred Colony
Kap, Y. S., Bus‐Spoor, C., van Driel, N., Dubbelaar, M. L., Grit, C., Kooistra, S. M., Fagrouch, Z. C., Verschoor, E. J., Bauer, J., Eggen, B. J. L., et al. (2018) · The Journal of Immunology · doi:10.4049/jimmunol.1800822 · Cited by 36
A high-throughput sequencing assay to comprehensively detect and characterize unicellular eukaryotes and helminths from biological and environmental samples
Cannon, M. V., Bogale, H. N., Rutt, L., Humphrys, M. S., Korpe, P. S., Duggal, P., Ravel, J., & Serre, D. (2018) · Microbiome · doi:10.1186/s40168-018-0581-6 · Cited by 37
Bioremediation of strontium and technetium contaminated groundwater using glycerol phosphate
Cleary, A., Lloyd, J. R., Newsome, L., Shaw, S., Boothman, C., Boshoff, G., Atherton, N., & Morris, K. (2019) · Chemical Geology · doi:10.1016/j.chemgeo.2019.02.004 · Cited by 37
Diversity and Characterization of Oomycetes Associated with Corn Seedlings in Michigan
Rojas, A. J., Witte, A., Noel, Z. A., Jacobs, J. L., & Chilvers, M. I. (2019) · Phytobiomes Journal · doi:10.1094/pbiomes-12-18-0059-r · Cited by 37
Antenatal Microbial Colonization of Mammalian Gut
Borghi, E., Massa, V., Severgnini, M., Fazio, G., Avagliano, L., Menegola, E., Bulfamante, G., Morace, G., & Borgo, F. (2018) · Reproductive Sciences · doi:10.1177/1933719118804411 · Cited by 38
Sex-related Alterations of Gut Microbiota in the C57BL/6 Mouse Model of Inflammatory Bowel Disease
Son, H. J., Kim, N., Song, C., Nam, R. H., Choi, S. I., Kim, J. S., & Lee, D. H. (2019) · Journal of Cancer Prevention · doi:10.15430/jcp.2019.24.3.173 · Cited by 37
Successful Fecal Microbiota Transplantation in a Patient Suffering From Irritable Bowel Syndrome and Recurrent Urinary Tract Infections
Hocquart, M., Pham, T., Kuete, E., Tomeï, E., Lagier, J., & Raoult, D. (2019) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofz398 · Cited by 37
Impact of lignans in oilseed mix on gut microbiome composition and enterolignan production in younger healthy and premenopausal women: an in vitro pilot study
Corona, G., Kreimes, A., Barone, M., Turroni, S., Brigidi, P., Keleszade, E., & Costabile, A. (2020) · Microbial Cell Factories · doi:10.1186/s12934-020-01341-0 · Cited by 38
Tracking seasonal changes in diversity of pollen allergen exposure: Targeted metabarcoding of a subtropical aerobiome
Campbell, B. C., Kouba, J. A., Timbrell, V. L., Noor, M. J., Massel, K., Gilding, E. K., Angel, N. Z., Kemish, B., Hugenholtz, P., Godwin, I. D., et al. (2020) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2020.141189 · Cited by 37
Effects of dietary fibers with different physicochemical properties on fermentation kinetics and microbial composition by fecal inoculum from lactating sows in vitro
Pi, Y., Hu, J., Bai, Y., Wang, Z., Wu, Y., Ye, H., Zhang, S., Tao, S., Xiao, Y., Han, D., et al. (2020) · Journal of the Science of Food and Agriculture · doi:10.1002/jsfa.10698 · Cited by 38
Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae
Keating, C., Bolton‐Warberg, M., Hinchcliffe, J., Davies, R., Whelan, S., Wan, A. H. L., FitzGerald, R. D., Davies, S. J., Ijaz, U. Z., & Smith, C. J. (2021) · Animal Microbiome · doi:10.1186/s42523-020-00065-1 · Cited by 36
Gut Microbiota Functional Dysbiosis Relates to Individual Diet in Subclinical Carotid Atherosclerosis
Baragetti, A., Severgnini, M., Olmastroni, E., Dioguardi, C. C., Mattavelli, E., Angius, A., Rotta, L., Cibella, J., Caredda, G., Consolandi, C., et al. (2021) · Nutrients · doi:10.3390/nu13020304 · Cited by 39
Cecal bacterial communities in wild Japanese rock ptarmigans and captive Svalbard rock ptarmigans
Ushida, K., Segawa, T., Tsuchida, S., & Murata, K. (2015) · Journal of Veterinary Medical Science · doi:10.1292/jvms.15-0313 · Cited by 37
Individualization of pubic hair bacterial communities and the effects of storage time and temperature
Williams, D. W., & Gibson, G. C. (2016) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2016.09.006 · Cited by 37
Assessment of gut microbiota populations in lean and obese Zucker rats
Hakkak, R., Korourian, S., Foley, S. L., & Erickson, B. D. (2017) · PLoS ONE · doi:10.1371/journal.pone.0181451 · Cited by 37
Analysis of Stored Wheat Grain-Associated Microbiota Reveals Biocontrol Activity among Microorganisms against Mycotoxigenic Fungi
Solanki, M. K., Abdelfattah, A., Sadhasivam, S., Zakin, V., Wisniewski, M., Droby, S., & Sionov, E. (2021) · Journal of Fungi · doi:10.3390/jof7090781 · Cited by 36
Contamination of long-term manure-fertilized Indian paddy soils with veterinary antibiotics: Impact on bacterial communities and antibiotics resistance genes
Kuppusamy, S., Venkateswarlu, K., Megharaj, M., Kanmani, S., & Lee, Y. B. (2023) · Applied Soil Ecology · doi:10.1016/j.apsoil.2023.105106 · Cited by 36
Methanobacterium enables high rate electricity-driven autotrophic sulfate reduction
Pozo, G., Jourdin, L., Lü, Y., Ledezma, P., Keller, J., & Freguia, S. (2015) · RSC Advances · doi:10.1039/c5ra18444d · Cited by 36
A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data
Zhang, Y., Sun, Y., & Cole, J. R. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003737 · Cited by 38
Meiobenthic community composition and biodiversity along a 5500 km transect of Western Antarctica: a metabarcoding analysis
Brannock, P. M., Learman, D. R., Mahon, A. R., Santos, S., & Halanych, K. M. (2018) · Marine Ecology Progress Series · doi:10.3354/meps12717 · Cited by 36
Clinical impact of measurable residual disease monitoring by ultradeep next generation sequencing in NPM1 mutated acute myeloid leukemia
Patkar, N. V., Kodgule, R., Kakirde, C., Raval, G., Bhanshe, P., Joshi, S., Chaudhary, S., Badrinath, Y., Ghoghale, S., Kadechkar, S., et al. (2018) · Oncotarget · doi:10.18632/oncotarget.26400 · Cited by 36
A Mediterranean Diet Mix Has Chemopreventive Effects in a Murine Model of Colorectal Cancer Modulating Apoptosis and the Gut Microbiota
Piazzi, G., Prossomariti, A., Baldassarre, M., Montagna, C., Vitaglione, P., Fogliano, V., Biagi, E., Candela, M., Brigidi, P., Balbi, T., et al. (2019) · Frontiers in Oncology · doi:10.3389/fonc.2019.00140 · Cited by 40
Processing and integration of functionally oriented prespacers in the Escherichia coli CRISPR system depends on bacterial host exonucleases
Ramachandran, A., Summerville, L., Learn, B. A., DeBell, L., & Bailey, S. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.012196 · Cited by 36
Future Climate Significantly Alters Fungal Plant Pathogen Dynamics during the Early Phase of Wheat Litter Decomposition
Wahdan, S. F. M., Hossen, S., Tanunchai, B., Schädler, M., Buscot, F., & Purahong, W. (2020) · Microorganisms · doi:10.3390/microorganisms8060908 · Cited by 36
PacBio sequencing output increased through uniform and directional fivefold concatenation
Kanwar, N., Blanco, C., Chen, I. A., & Seelig, B. (2021) · Scientific Reports · doi:10.1038/s41598-021-96829-z · Cited by 38
Exogenous Fecal Microbial Transplantation Alters Fearfulness, Intestinal Morphology, and Gut Microbiota in Broilers
Yan, C., Xiao, J., Li, Z., Liu, H., Zhao, X., Liu, J., Chen, S., & Zhao, X. (2021) · Frontiers in Veterinary Science · doi:10.3389/fvets.2021.706987 · Cited by 36
Tea polyphenols protect mice from acute ethanol-Induced liver injury by modulating the gut microbiota and short-chain fatty acids
Sun, Y., Kang, K., Li, Y., Sang, L.-X., & Chang, B. (2021) · Journal of Functional Foods · doi:10.1016/j.jff.2021.104865 · Cited by 36
Maternal regulation of biliary disease in neonates via gut microbial metabolites
Jee, J. J., Yang, L., Shivakumar, P., Xu, P.-P., Mourya, R., Thanekar, U., Yu, P., Zhu, Y., Pan, Y., Wang, H., et al. (2022) · Nature Communications · doi:10.1038/s41467-021-27689-4 · Cited by 37
Phylogenetic and functional diversity of Chrysophyceae in inland waters
Böck, C., Olefeld, J. L., Vogt, J. C., Albach, D. C., & Boenigk, J. (2022) · Organisms Diversity & Evolution · doi:10.1007/s13127-022-00554-y · Cited by 36
Comparative bacterial community analysis in relatively pristine and anthropogenically influenced mangrove ecosystems on the Red Sea
Ullah, R., Yasir, M., Khan, I., Bibi, F., Sohrab, S. S., Al-Ansari, A. M., Al-Abbasi, F. A., Al-Sofyani, A., Daur, İ., Lee, S., et al. (2017) · Canadian Journal of Microbiology · doi:10.1139/cjm-2016-0587 · Cited by 35
Increased water colour affects freshwater plankton communities in a mesocosm study
Lebret, K., Langenheder, S., Colinas, N., Östman, Ö., & Lindström, E. S. (2017) · Aquatic Microbial Ecology · doi:10.3354/ame01858 · Cited by 35
In-feed resin acids reduce matrix metalloproteinase activity in the ileal mucosa of healthy broilers without inducing major effects on the gut microbiota
Aguirre, M., Vuorenmaa, J., Valkonen, E., Kettunen, H., Callens, C., Haesebrouck, F., Ducatelle, R., Immerseel, F. V., & Goossens, E. (2019) · Veterinary Research · doi:10.1186/s13567-019-0633-3 · Cited by 35
Widespread occurrence of asexual reproduction in higher termites of the Termes group (Termitidae: Termitinae)
Hellemans, S., Dolejšová, K., Křivánek, J., Fournier, D., Hanus, R., & Roisin, Y. (2019) · BMC Evolutionary Biology · doi:10.1186/s12862-019-1459-3 · Cited by 35
Eukaryotic influence on the oceanic biological carbon pump in the Scotia Sea as revealed by 18S rRNA gene sequencing of suspended and sinking particles
Duret, M. T., Lampitt, R. S., & Lam, P. (2019) · Limnology and Oceanography · doi:10.1002/lno.11319 · Cited by 35
Manganese and cobalt redox cycling in laterites; Biogeochemical and bioprocessing implications
Newsome, L., Solano-Arguedas, A. F., Coker, V. S., Boothman, C., & Lloyd, J. R. (2019) · Chemical Geology · doi:10.1016/j.chemgeo.2019.119330 · Cited by 36
Taxonomic profiling of bacteria and fungi in freshwater sewer receiving hospital wastewater
Ogwugwa, V. H., Oyetibo, G. O., & Amund, O. O. (2020) · Environmental Research · doi:10.1016/j.envres.2020.110319 · Cited by 35
Exposure to high fructose corn syrup during adolescence in the mouse alters hepatic metabolism and the microbiome in a sex‐specific manner
Bhat, S., Pinney, S. E., Kennedy, K. M., McCourt, C. R., Mundy, M. A., Surette, M. G., Sloboda, D. M., & Simmons, R. A. (2021) · The Journal of Physiology · doi:10.1113/jp280034 · Cited by 35
Metagenomics of mine tailing rhizospheric communities and its selection for plant establishment towards bioremediation
Romero, M. F., Gallego, D., Blaz, J., Lechuga, A., Martínez, J. F., Barajas, H. R., Hayano‐Kanashiro, C., Peimbert, M., Cruz‐Ortega, R., Molina‐Freaner, F. E., et al. (2021) · Microbiological Research · doi:10.1016/j.micres.2021.126732 · Cited by 36
Is Gut Microbiota a Key Player in Epilepsy Onset? A Longitudinal Study in Drug-Naive Children
Ceccarani, C., Viganò, I., Ottaviano, E., Redaelli, M. G., Severgnini, M., Vignoli, A., & Borghi, E. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.749509 · Cited by 36
Neoagarooligosaccharides modulate gut microbiota and alleviate body weight gain and metabolic syndrome in high-fat diet-induced obese rats
Oh, J. K., Vasquez, R., Kim, S. H., Lee, J. H., Kim, E. J., Hong, S., & Kang, D. (2021) · Journal of Functional Foods · doi:10.1016/j.jff.2021.104869 · Cited by 34
Land-use change affects the diversity and functionality of soil bacterial communities in semi-arid Chaco region, Argentina
Viruel, E., Fontana, C. A., Puglisi, E., Nasca, J., Banegas, N., & Cocconcelli, P. S. (2021) · Applied Soil Ecology · doi:10.1016/j.apsoil.2021.104362 · Cited by 35
First insights into the living groundwater mycobiome of the terrestrial biogeosphere
Nawaz, A., Purahong, W., Lehmann, R. G., Herrmann, M., Totsche, K. U., Küsel, K., Wubet, T., & Buscot, F. (2018) · Water Research · doi:10.1016/j.watres.2018.07.067 · Cited by 38
Human norovirus hyper-mutation revealed by ultra-deep sequencing
Cuevas, J. M., Combe, M., Torres‐Puente, M., Garijo, R., Guix, S., Buesa, J., Rodríguez‐Díaz, J., & Sanjuán, R. (2016) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2016.04.017 · Cited by 33
IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data
Mysara, M., Leys, N., Raes, J., & Monsieurs, P. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1061-2 · Cited by 34
Biogeography of soil Thaumarchaeota in relation to soil depth and land usage
Lu, X., Seuradge, B. J., & Neufeld, J. D. (2016) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiw246 · Cited by 34
Self-citation
Human Catestatin Alters Gut Microbiota Composition in Mice
Rabbi, M. F., Munyaka, P. M., Eissa, N., Metz‐Boutigue, M., Khafipour, E., & Ghia, J. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.02151 · Cited by 35
Adverse effect of early-life high-fat/high-carbohydrate (“Western”) diet on bacterial community in the distal bowel of mice
Villamil, S. I., Huerlimann, R., Morianos, C., Sarnyai, Z., & Maes, G. E. (2017) · Nutrition Research · doi:10.1016/j.nutres.2017.11.008 · Cited by 36
Creek to Table: Tracking fecal indicator bacteria, bacterial pathogens, and total bacterial communities from irrigation water to kale and radish crops
Allard, S. M., Callahan, M. T., Bui, A. Q., Ferelli, A. M. C., Chopyk, J., Chattopadhyay, S., Mongodin, E. F., Micallef, S. A., & Sapkota, A. R. (2019) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2019.02.179 · Cited by 38
A centromere satellite concomitant with extensive karyotypic diversity across the Peromyscus genus defies predictions of molecular drive
Smalec, B. M., Heider, T. N., Flynn, B. L., & O'Neill, R. J. W. (2019) · Chromosome Research · doi:10.1007/s10577-019-09605-1 · Cited by 34
Fecal microbiota transplantation prevents Candida albicans from colonizing the gastrointestinal tract
Matsuo, K., Haku, A., Bi, B., Takahashi, H., Kamada, N., Yaguchi, T., Saijo, S., Yoneyama, M., & Goto, Y. (2019) · Microbiology and Immunology · doi:10.1111/1348-0421.12680 · Cited by 36
The role of sedimentation in the structuring of microbial communities in biofloc-dominated aquaculture tanks
Schveitzer, R., Fonseca, G., Orteney, N. E., Copetti, F., Thompson, F. L., Thompson, C. C., & Gregoracci, G. B. (2019) · Aquaculture · doi:10.1016/j.aquaculture.2019.734493 · Cited by 34
Protective effect of Bacillus amyloliquefaciens against Salmonella via polarizing macrophages to M1 phenotype directly and to M2 depended on microbiota
Fu, A., Mo, Q., Wu, Y., Wang, B., Liu, R., Tang, L., Zeng, Z., Zhang, X., & Li, W. (2019) · Food & Function · doi:10.1039/c9fo01651a · Cited by 35
Draft genome of Tanacetum cinerariifolium, the natural source of mosquito coil
Yamashiro, T., Shiraishi, A., Satake, H., & Nakayama, K. (2019) · Scientific Reports · doi:10.1038/s41598-019-54815-6 · Cited by 34
Different Effects of Soil Fertilization on Bacterial Community Composition in the Penicillium canescens Hyphosphere and in Bulk Soil
Zhang, Y., Hao, X., García-Lemos, A. M., Nunes, I., Nicolaisen, M. H., & Nybroe, O. (2020) · Applied and Environmental Microbiology · doi:10.1128/aem.02969-19 · Cited by 34
Mucosal Microbiota and Metabolome along the Intestinal Tract Reveal a Location-Specific Relationship
Yuan, C., Graham, M. L., Staley, C. M., & Subramanian, S. (2020) · mSystems · doi:10.1128/msystems.00055-20 · Cited by 32

Authors: Masella, A. P., Bartram, A. K., Truszkowski, J. M., Brown, D. G., & Neufeld, J. D.
Affiliations: University of Waterloo (CA)
Corresponding author: Neufeld, Josh D
ORCID: Truszkowski, Jakub M
Brown, Daniel G
Neufeld, Josh D
Venue: BMC Bioinformatics
Publisher: Springer Science and Business Media LLC
Published: 2012-02-14
Volume: 13
Issue: 1
Pages: 31-31
ISSN: 1471-2105 (ISSN-L)
DOI: 10.1186/1471-2105-13-31
PMC: PMC3471323
OpenAlex: W2132548846
Cited by: 2,132
References: 12
Citations by year: 2026: 61 · 2025: 89 · 2024: 90 · 2023: 115 · 2022: 187 · 2021: 254 · 2020: 277 · 2019: 264 · 2018: 251 · 2017: 204 · 2016: 152 · 2015: 108 · 2014: 56 · 2013: 21 · 2012: 3
FWCI: 24.15
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
Locations: BMC Bioinformatics (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders: Government of Ontario
Natural Sciences and Engineering Research Council of Canada
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Physical Sciences › Mathematics › Theoretical Computer Science › Algorithms and Data Compression
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords: 16S rRNA gene, microbial community analysis, error correction, amplicon sequencing, sequencing errors
MeSH terms: Bacteria, RNA, Bacterial, RNA, Ribosomal, 16S, Software, Metagenomics

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

PANDAseq: paired-end assembler for illumina sequences

Abstract

Overview

Integrity signals

Figures

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks