Cited by 1,357Genomics and Phylogenetic StudiesFractal and DNA sequence analysisGenetics, Bioinformatics, and Biomedical Research

The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

Open access

Cox, Murray P, Peterson, Daniel A, Biggs, Patrick J·2010·BMC Bioinformatics

DOI 10.1186/1471-2105-11-485PMC PMC2956736

Open this paper in CoChat — free account Open PDF

Abstract

BACKGROUND: Illumina's second-generation sequencing platform is playing an increasingly prominent role in modern DNA and RNA sequencing efforts. However, rapid, simple, standardized and independent measures of run quality are currently lacking, as are tools to process sequences for use in downstream applications based on read-level quality data. RESULTS: We present SolexaQA, a user-friendly software package designed to generate detailed statistics and at-a-glance graphics of sequence data quality both quickly and in an automated fashion. This package contains associated software to trim sequences dynamically using the quality scores of bases within individual reads. CONCLUSION: The SolexaQA package produces standardized outputs within minutes, thus facilitating ready comparison between flow cell lanes and machine runs, as well as providing immediate diagnostic information to guide the manipulation of sequence data for downstream analyses.

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 · 10.1186/1471-2105-11-485

Cites

9 of 9 references verified0 citation errors · 0 not checkable

Statistics

Figure 1 Example heat map showing several commonly observed quality defects. Nucleotide positions 1-75 are plotted from left-to-right along the x-axis; tiles 1-100 are ranked from top-to-bottom along the y-axis. (These numbers may vary for other datasets). The scale depicts the mean probability of observing a base call error for each tile at each nucleotide position. The defects evident in this dataset (see text for details) are atypical of Illumina sequencing; this dataset was chosen specifically to illustrate the capabilities of SolexaQA.CC BY · PubMed Central

Figure 2 Distribution of mean quality (probability of error, y-axis) at each nucleotide position (x-axis) for each tile individually (dotted black lines) and the entire dataset combined (red circles). Note the considerable variance in data quality between tiles. The defects evident in this dataset (see text for details) are atypical of Illumina sequencing; this dataset was chosen specifically to illustrate the capabilities of SolexaQA.CC BY · PubMed Central

Figure 3 Distribution of longest read segments passing a user-defined quality threshold (here, P = 0.05, or equivalently, Phred quality score Q ≈ 13, or a base call error rate of 1-in-20). Note that reads in this dataset would be trimmed on average to ~25 nucleotides (i.e., only approximately one-third of the initial 75 nucleotide read length). The defects evident in this dataset (see text for details) are atypical of Illumina sequencing; this dataset was chosen specifically to illustrate the capabilities of SolexaQA.CC BY · PubMed Central

Figure 4 Effect of dynamically trimmed versus untrimmed reads on de novo assembly with the Velvet assembler. Dynamically trimmed reads (solid symbols) relative to untrimmed reads (open symbols) yield improved N50 values (red squares) and maximum contig sizes (blue triangles). Summary statistics were averaged across de novo assemblies for 20 isolates of Campylobacter coli and C. jejuni, and normalized by the total number of reads employed in each assembly.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.

R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,893
Velvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,575
Sequencing technologies – the next generation
Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066
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
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
Dohm, J. C., Lottaz, C., Borodina, T., & Himmelbauer, H. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn425 · Cited by 1,088
Matrix2png: a utility for visualizing matrix data
Pavlidis, P., & Noble, W. S. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.295 · Cited by 345
Probabilistic base calling of Solexa sequencing data
Rougemont, J., Amzallag, A., Iseli, C., Farinelli, L., Xénarios, I., & Naef, F. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-431 · Cited by 104
PIQA: pipeline for Illumina G1 genome analyzer data quality assessment
Martinez-Alcántara, A., Ballesteros, E., Feng, C., Rojas, M., Koshinsky, H. A., Fofanov, V. Y., Havlak, P., & Fofanov, Y. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp429 · Cited by 50
TileQC: A system for tile-based quality control of Solexa data
Dolan, P. C., & Denver, D. R. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-250 · Cited by 38

Show all 9 references

Sorted by citations

Items 801–900 of 1,000

De novo transcriptome analysis of carotenoid and polyunsaturated fatty acid metabolism in Rhodomonas sp.
Li, H., Wang, W., Wang, Z., Lin, X., Zhang, F., & Yang, L. (2015) · Journal of Applied Phycology · doi:10.1007/s10811-015-0703-5 · Cited by 12
Wind-driven distribution of bacteria in coastal Antarctica: evidence from the Ross Sea region
Bowman, J. S., & Deming, J. W. (2016) · Polar Biology · doi:10.1007/s00300-016-1921-2 · Cited by 12
An analysis of the role of the ShSUT1 sucrose transporter in sugarcane using RNAi suppression
Glassop, D., Stiller, J., Bonnett, G. D., Grof, C. P. L., & Rae, A. L. (2017) · Functional Plant Biology · doi:10.1071/fp17073 · Cited by 12
Hymenoptera Genome Database: Using HymenopteraMine to Enhance Genomic Studies of Hymenopteran Insects
Elsik, C. G., Tayal, A., Unni, D. R., Burns, G. W., & Hagen, D. E. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7737-6_17 · Cited by 12
Knockout of the Hmt1p Arginine Methyltransferase in Saccharomyces cerevisiae Leads to the Dysregulation of Phosphate-associated Genes and Processes
Chia, S. Z., Lai, Y.-W., Yagoub, D., Lev, S., Hamey, J. J., Pang, C. N. I., Desmarini, D., Chen, Z., Djordjevic, J. T., Erce, M. A., et al. (2018) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra117.000214 · Cited by 13
Evidence for frequency‐dependent selection maintaining polymorphism in the Batesian mimic Papilio polytes in multiple islands in the Ryukyus, Japan
Tsurui‐Sato, K., Sato, Y., Kato, E., Katoh, M., Kimura, R., Tatsuta, H., & Tsuji, K. (2019) · Ecology and Evolution · doi:10.1002/ece3.5182 · Cited by 12
Unique Clindamycin-Resistant Clostridioidesdifficile Strain Related to Fluoroquinolone-Resistant Epidemic BI/RT027 Strain
Skinner, A. M., Petrella, L. A., Siddiqui, F., Sambol, S. P., Gulvik, C. A., Gerding, D. N., Donskey, C. J., & Johnson, S. (2019) · Emerging infectious diseases · doi:10.3201/eid2602.181965 · Cited by 12
Development of Kompetitive Allele Specific PCR markers for identification of persimmon varieties using genotyping-by-sequencing
Ma, K. B., Yang, S.-J., Jo, Y., Kang, S. S., & Nam, M. (2020) · Electronic Journal of Biotechnology · doi:10.1016/j.ejbt.2020.11.003 · Cited by 12
Identification and analysis of a differentially expressed wheat RING-type E3 ligase in spike primordia development during post-vernalization
Kim, J. H., Khan, I. U., Lee, C. W., Kim, D. Y., Jang, C. S., Lim, S. D., Park, Y. C., Kim, J. H., & Seo, Y. W. (2021) · Plant Cell Reports · doi:10.1007/s00299-020-02651-8 · Cited by 12
Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya
Muturi, S. M., Muthui, L., Njogu, P. M., Onguso, J. M., Wachira, F. N., Opiyo, S. O., & Pellé, R. (2021) · PLoS ONE · doi:10.1371/journal.pone.0244755 · Cited by 12
Fish environmental DNA in Tokyo Bay: A feasibility study on the availability of environmental DNA for fisheries
Hongo, Y., Nishijima, S., Kanamori, Y., Sawayama, S., Yokouchi, K., Kanda, N., Oori, S., Uto, Y., Ishii, M., Mita, H., et al. (2021) · Regional Studies in Marine Science · doi:10.1016/j.rsma.2021.101950 · Cited by 12
Nitric oxide production and scavenging in waterlogged roots of rape seedlings
Lee, Y., Kim, K.-S., Jang, Y., & Choi, I.-H. (2014) · Genes & Genomics · doi:10.1007/s13258-014-0202-0 · Cited by 12
The Transcriptomes of the Crucian Carp Complex (Carassius auratus) Provide Insights into the Distinction between Unisexual Triploids and Sexual Diploids
Li, C., Li, J.-T., Kuang, Y., Xu, R., Zhao, Z., Hou, G., Liang, H., & Sun, X. (2014) · International Journal of Molecular Sciences · doi:10.3390/ijms15069386 · Cited by 12
Evolution and adaptation of SAR11 and Cyanobium in a saline Tibetan lake
Oh, S., Zhang, R., Wu, Q. L., & Liu, W. (2016) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12408 · Cited by 11
Microbiome of the Southwestern Atlantic invasive scleractinian coral, Tubastraea tagusensis
Zanotti, A. A., Gregoracci, G. B., Capel, K. C. C., & Kitahara, M. V. (2020) · Animal Microbiome · doi:10.1186/s42523-020-00047-3 · Cited by 12
Analysis of Genetic Diversity in Adzuki Beans (Vigna angularis): Insights into Environmental Adaptation and Early Breeding Strategies for Yield Improvement
Wang, X.-H., Choi, Y., Jeon, Y., Yi, J.-Y., Shin, M., Desta, K. T., & Yoon, H. (2023) · Plants · doi:10.3390/plants12244154 · Cited by 11
Leveraging genomics and phenomics to accelerate improvement in mungbean: A case study in how to go from GWAS to selection
Fumia, N., Nair, R. M., Lin, Y., Lee, C., Chen, H., von Wettberg, E., Kantar, M. B., & Schafleitner, R. (2023) · The Plant Phenome Journal · doi:10.1002/ppj2.20088 · Cited by 11
Exploring bacterial diversity in Arctic fjord sediments: a 16S rRNA–based metabarcoding portrait
Kachiprath, B., Solomon, S., Gopi, J., Jayachandran, P. R., Jabir, T., Sarasan, M., Mohan, A. S., Puthumana, J., Chaithanya, E. R., & Philip, R. (2024) · Brazilian Journal of Microbiology · doi:10.1007/s42770-023-01217-6 · Cited by 11
Influence of vegetation and substrate type on removal of emerging organic contaminants and microbial dynamics in horizontal subsurface constructed wetlands
Wolff, D., Abou-Kandil, A., Azaizeh, H., Wick, A., & Jadoun, J. (2024) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2024.172346 · Cited by 11
A study at the wildlife-livestock interface unveils the potential of feral swine as a reservoir for extended-spectrum β-lactamase-producing Escherichia coli
Liu, T., Lee, S.-Y., Kim, M., Fan, P. F., Boughton, R. K., Boucher, C. A., & Jeong, K. C. (2024) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2024.134694 · Cited by 11
Comparison of Bioinformatic Pipelines for eDNA Metabarcoding Data Analysis of Fish Populations
dos Santos, R. A., & Blabolil, P. (2025) · Fishes · doi:10.3390/fishes10050214 · Cited by 11
Identification of Bone Metastasis-associated Genes of Gastric Cancer by Genome-wide Transcriptional Profiling
Lin, M.-Z., Li, X., Guo, H., Ji, F., Ye, L., Ma, X., & Cheng, W. (2017) · Current Bioinformatics · doi:10.2174/1574893612666171121154017 · Cited by 11
Species composition and overall diversity are significantly correlated between the tongue coating and gastric fluid microbiomes in gastritis patients
Cui, J., Hou, S., Liu, B., Yang, M., Wei, L., Du, S., & Li, S. (2022) · BMC Medical Genomics · doi:10.1186/s12920-022-01209-9 · Cited by 11
Targeted exome sequencing reveals novel USH2A mutations in Chinese patients with simplex Usher syndrome
Shu, H.-R., Bi, H., Pan, Y., Xu, H., Song, J., & Hu, J. (2015) · BMC Medical Genetics · doi:10.1186/s12881-015-0223-9 · Cited by 11
Complete genome sequencing and analysis of Capsicum annuum varieties
Ahn, Y., Karna, S., Jun, T., Yang, E.-Y., Lee, H., Kim, J., & Kim, J. (2016) · Molecular Breeding · doi:10.1007/s11032-016-0557-9 · Cited by 11
Transcriptome analysis of gill from Lateolabrax maculatus and aqp3 gene expression
Shen, Y., He, Y. D., Bi, Y., Chen, J., Zhao, Z., Li, J., & Chen, X. (2019) · Aquaculture and Fisheries · doi:10.1016/j.aaf.2019.03.004 · Cited by 11
Genetic relationships and population structure of pears (Pyrus spp.) assessed with genome-wide SNPs detected by genotyping-by-sequencing
Kim, K., Oh, Y., Han, H., Oh, S., Lim, H., Chung, J., Kim, Y.-K., & Kim, D. (2019) · Horticulture Environment and Biotechnology · doi:10.1007/s13580-019-00178-w · Cited by 11
Metagenomics Uncovers a Core SAR11 Population in Brackish Surface Waters of the Baltic Sea
Vidanage, P. W., Ko, S., & Oh, S. (2020) · Water · doi:10.3390/w12020501 · Cited by 11
Draft Genome Sequence of the Thermophilic Bacterium Bacillus licheniformis SMIA-2, an Antimicrobial- and Thermostable Enzyme-Producing Isolate from Brazilian Soil
Bernardo, S. P. C., Rosana, A. R. R., de Souza, A. N., Chiorean, S., Martins, M. L. L., & Vederas, J. C. (2020) · Microbiology Resource Announcements · doi:10.1128/mra.00106-20 · Cited by 11
Chromosome Architecture and Gene Content of the Emergent Pathogen Acinetobacter haemolyticus
Castro-Jaimes, S., Bello‐López, E., Velázquez-Acosta, C., Volkow-Fernández, P. A., Lozano-Zaraín, P., Castillo‐Ramírez, S., & Cevallos, M. A. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00926 · Cited by 11
Functional diversity of bacterial communities in the rhizosphere of maize grown on a soil under organic and inorganic fertilization
Enebe, M. C., & Babalola, O. O. (2022) · Scientific African · doi:10.1016/j.sciaf.2022.e01212 · Cited by 11
Intracellular Ca2+ and K+ concentration in Brassica oleracea leaf induces differential expression of transporter and stress-related genes
Lee, J., Kim, J., Choi, J., Lee, M., Kim, M.-K., Lee, Y. H., Hur, Y., Nou, I., Park, S. U., Min, S. R., et al. (2016) · BMC Genomics · doi:10.1186/s12864-016-2512-x · Cited by 11
Subfunctionalization influences the expansion of bacterial multidrug antibiotic resistance
Perrin, E., Fondi, M., Bosi, E., Mengoni, A., Buroni, S., Scoffone, V. C., Valvano, M. A., & Fani, R. (2017) · BMC Genomics · doi:10.1186/s12864-017-4222-4 · Cited by 11
Studying the Microbiome of Cyanobacterial Biocrusts From Drylands and Its Functional Influence on Biogeochemical CyclesPreprint
Miralles, I., Ortega, R., & Montero‐Calasanz, M. D. C. (2021) · Research Square · doi:10.21203/rs.3.rs-252045/v1 · Cited by 11
Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae
Xiaokaiti, X., Hashiguchi, Y., Ota, H., & Kumazawa, Y. (2022) · Genes · doi:10.3390/genes13081470 · Cited by 10
Caecal microbial communities, functional diversity, and metabolic pathways in Ross 308 broiler chickens fed with diets containing different levels of Marama (Tylosema esculentum) bean meal
Montso, P. K., Mnisi, C. M., & Ayangbenro, A. S. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1009945 · Cited by 10
A GBS-based genetic linkage map and quantitative trait loci (QTL) associated with resistance to Xanthomonas campestris pv. campestris race 1 identified in Brassica oleracea
Lu, L., Choi, S. R., Lim, Y. P., Kang, S., & Yi, S. Y. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2023.1205681 · Cited by 10
Genome-Wide Association Study of Phenolic Content and Antioxidant Properties in Eggplant Germplasm
Ro, N., Haile, M., Ko, H.-C., Cho, G., Lee, J. R., Kim, B., Lee, S., & Kim, S. (2023) · Genes · doi:10.3390/genes14071315 · Cited by 10
Adoption and impact of improved amaranth cultivars in Tanzania using DNA fingerprinting
Wanyama, R., Schreinemachers, P., Ochieng, J., Bwambo, O., Alphonce, R., Dinssa, F. F., Lin, Y., & Schafleitner, R. (2023) · Food Security · doi:10.1007/s12571-023-01378-0 · Cited by 10
Complete Genome Sequence of Campylobacter concisus ATCC 33237 T and Draft Genome Sequences for an Additional Eight Well-Characterized C. concisus Strains
Cornelius, A. J., Miller, W. G., Lastovica, A. J., On, S. L. W., French, N. P., Vandenberg, O., & Biggs, P. J. (2017) · Genome Announcements · doi:10.1128/genomea.00711-17 · Cited by 10
Self-citation
A novel mutation of FOXC1 in a Chinese family with Axenfeld‑Rieger syndrome
Wu, X., Xie, H., Wu, T., Liu, W., Chen, L., Li, Z., Wang, D., Wang, Y., & Huang, H. (2019) · Experimental and Therapeutic Medicine · doi:10.3892/etm.2019.7789 · Cited by 10
Diversity and abundance of the functional genes and bacteria associated with RDX degradation at a contaminated site pre- and post-biostimulation
Dang, H., & Cupples, A. M. (2021) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-021-11457-x · Cited by 10
Metagenomics indicate that public health risk may be higher from flooding following dry versus rainy periods
Kim, M., Kienast, Y., Hatt, J. K., Kirby, A. E., & Konstantinidis, K. T. (2022) · Environmental Microbiology Reports · doi:10.1111/1758-2229.13047 · Cited by 10
A biallelic loss of function variant in HORMAD1 within a large consanguineous Turkish family is associated with spermatogenic arrest
Okutman, Ö., Boivin, M., Muller, J., Charlet‐Berguerand, N., & Viville, S. (2022) · Human Reproduction · doi:10.1093/humrep/deac259 · Cited by 10
Effects of metal contamination with physicochemical properties on the sediment microbial communities in a tropical eutrophic-hypereutrophic urban reservoir in Brazil
Pierangeli, G. M. F., da Silva, K. M. R., Coelho, L. H. G., Benassi, R. F., Domingues, M. R., & Gregoracci, G. B. (2023) · Environmental Science and Pollution Research · doi:10.1007/s11356-023-26114-1 · Cited by 10
Population genomics of diarrheagenic Escherichia coli uncovers high connectivity between urban and rural communities in Ecuador
Rothstein, A. P., Jesser, K. J., Feistel, D. J., Konstantinidis, K. T., Trueba, G. A., & Lévy, K. (2023) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2023.105476 · Cited by 10
A DNA-based diagnostic for differentiating among New Zealand endemic Podocarpus
Marshall, C. W., Chagné, D., Deusch, O., Gruenheit, N., McCallum, J. A., Bergin, D. O., Lockhart, P. J., & Wilcox, P. L. (2015) · Tree Genetics & Genomes · doi:10.1007/s11295-015-0888-4 · Cited by 10
Transcriptional adaptation of Shigella flexneri during adherence to epithelial cells
Ni, Z., Jiang, L., Feng, L., Wang, L., & Liu, B. (2014) · Journal of Basic Microbiology · doi:10.1002/jobm.201400414 · Cited by 9
Comparative genomic and proteomic analyses of Clostridium acetobutylicum Rh8 and its parent strain DSM 1731 revealed new understandings on butanol tolerance
Bao, G., Dong, H., Zhu, Y., Mao, S., Zhang, T., Zhang, Y., Chen, Z., & Li, Y. (2014) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2014.07.052 · Cited by 10
Sticky Genomes: Using NGS Evidence to Test Hybrid Speciation Hypotheses
Morgan‐Richards, M., Hills, S. F. K., Biggs, P. J., & Trewick, S. A. (2016) · PLoS ONE · doi:10.1371/journal.pone.0154911 · Cited by 10
Self-citation
Transcriptome profiles of embryos before and after cleavage in Eriocheir sinensis: identification of developmental genes at the earliest stages
Hui, M., Cui, Z., Liu, Y. M., & Song, C. (2016) · Chinese Journal of Oceanology and Limnology · doi:10.1007/s00343-017-5364-6 · Cited by 10
Deregulation of the planar cell polarity genes CELSR3 and FZD3 in Hirschsprung disease
Su, L., Zhang, Z., Gan, L., Jiang, Q., Xiao, P., Zou, J., Li, Q., & Jiang, H. (2016) · Experimental and Molecular Pathology · doi:10.1016/j.yexmp.2016.09.003 · Cited by 10
Detection of CYP2C19 Genetic Variants in Malaysian Orang Asli from Massively Parallel Sequencing Data
Ang, G. Y., Yu, C. Y., Subramaniam, V., Khalid, M. I. H. A., Aziz, T. A. T. A., James, R. J., Ahmad, A., Rahman, T. H. A., Nor, F. M., Ismail, A. I., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0164169 · Cited by 10
Variation and evolution of polyadenylation profiles in sauropsid mitochondrial mRNAs as deduced from the high-throughput RNA sequencing
Sun, Y., Kurisaki, M., Hashiguchi, Y., & Kumazawa, Y. (2017) · BMC Genomics · doi:10.1186/s12864-017-4080-0 · Cited by 10
Taxonomic and Functional Annotation of Termite Degraded Butea monosperma (Lam.) Kuntze (Flame of the Forest)
Kumar, A., Vyas, P., Malla, M. A., & Dubey, A. (2019) · The Open Microbiology Journal · doi:10.2174/1874285801913010154 · Cited by 10
Characterization and genetic diversity of Dioscorea bacilliform viruses present in a Pacific yam germplasm collection
Sukal, A. C., Kidanemariam, D., Dale, J. L., Harding, R. M., & James, A. P. (2019) · Plant Pathology · doi:10.1111/ppa.13133 · Cited by 10
Comparative analysis of mitochondrial genome and expression variation between UG93A and UG93B reveals a candidate gene related to cytoplasmic male sterility in kenaf
Liao, X., Wei, M., Khan, A., Zhao, Y., Kong, X., Zhou, B., Li, M., Peng, S., Munsif, F., Ullah, A., et al. (2020) · Industrial Crops and Products · doi:10.1016/j.indcrop.2020.112502 · Cited by 10
Microbial diversity in water and animal faeces: a metagenomic analysis to assess public health risk
Phiri, B. J., Hayman, D. T. S., Biggs, P. J., French, N. P., & García–R, J. C. (2020) · New Zealand Journal of Zoology · doi:10.1080/03014223.2020.1831556 · Cited by 10
Self-citation
Identification of Genes Involved in the Synthesis of the Fungal Cell Wall Component Nigeran and Regulation of Its Polymerization in Aspergillus luchuensis
Uechi, K., Yaguchi, H., Tokashiki, J., Taira, T., & Mizutani, O. (2021) · Applied and Environmental Microbiology · doi:10.1128/aem.01144-21 · Cited by 10
A Novel Pear Scab (Venturia nashicola) Resistance Gene, Rvn3, from Interspecific Hybrid Pear (Pyrus pyrifolia × P. communis)
Oh, S., Han, H., & Kim, D. (2021) · Plants · doi:10.3390/plants10122632 · Cited by 10
Biofilm-Growing Bacteria Involved in the Corrosion of Concrete Wastewater Pipes: Protocols for Comparative Metagenomic Analyses
Gomez‐Alvarez, V. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0467-9_23 · Cited by 10
Reduced Virulence of an Introduced Forest Pathogen over 50 Years
Bradshaw, R. E., Ormond, S., Dupont, P., Chettri, P., Ozturk, I. K., McDougal, R. L., Bulman, L. S., & Cox, M. P. (2019) · Microorganisms · doi:10.3390/microorganisms7100420 · Cited by 10
Self-citation
Pyrosequencing and phenotypic microarray to decipher bacterial community variation in Sorghum bicolor (L.) Moench rhizosphere
Kumar, A., Dubey, A., Malla, M. A., & Dames, J. F. (2021) · Current Research in Microbial Sciences · doi:10.1016/j.crmicr.2021.100025 · Cited by 10
Proto-sex locus in large yellow croaker provides insights into early evolution of the sex chromosomePreprint
Wang, Z.-Y., Xiao, S.-J., Cai, M.-Y., Han, Z.-F., Li, W.-B., Xie, Y.-J., Xu, G.-C., Lin, A., Zhang, Y., Ye, K., et al. (2020) · bioRxiv · doi:10.1101/2020.06.23.166249 · Cited by 11
Cooperative role of AtRsmD and AtRimM proteins in modification and maturation of 16S rRNA in plastids
Liu, K., Lee, K. P., Duan, J., Kim, E. Y., Singh, R. M., Di, M., Meng, Z., & Kim, C. (2023) · The Plant Journal · doi:10.1111/tpj.16135 · Cited by 9
Co-Selection of Bacterial Metal and Antibiotic Resistance in Soil Laboratory Microcosms
Heydari, A., Kim, N. D., Biggs, P. J., Horswell, J., Gielen, G. J. H. P., Siggins, A., Taylor, M. D., Bromhead, C., & Palmer, B. R. (2023) · Antibiotics · doi:10.3390/antibiotics12040772 · Cited by 9
Self-citation
Differential interactions of Rickettsia species with tick microbiota in Rh. sanguineus and Rh. turanicus
Maître, A., Kratou, M., Corona-Guerrero, I., Abuin‐Denis, L., Mateos‐Hernández, L., Mosqueda, J., Almazán, C., Saïd, M. B., Piloto‐Sardiñas, E., Obregón, D., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-71539-4 · Cited by 9
Bio-electrochemical denitrification – The impact of cathode potential, inoculum source and nitrate loading rate
Laidin, D., Gostomski, P. A., Marshall, A. T., & Carere, C. R. (2025) · Journal of Water Process Engineering · doi:10.1016/j.jwpe.2025.108923 · Cited by 9
Next-generation sequencing-based transcriptome analysis of l-lysine-producing Corynebacterium glutamicum ATCC 21300 strain
Kim, H.-I., Nam, J.-Y., Cho, J., Lee, C., & Park, Y. (2013) · The Journal of Microbiology · doi:10.1007/s12275-013-3236-0 · Cited by 9
Diversity and distribution of benthic dinoflagellates in Tonga include the potentially harmful genera Gambierdiscus and Fukuyoa
Argyle, P., Rhodes, L. L., Smith, K. F., Harwood, D. T., Halafihi, T., & Marsden, I. D. (2023) · Harmful Algae · doi:10.1016/j.hal.2023.102524 · Cited by 9
Seasonal diet partition among top predators of a small island, Iriomote Island in the Ryukyu Archipelago, Japan
Tobe, A., Sato, Y., Wachi, N., Nakanishi, N., & Izawa, M. (2024) · Scientific Reports · doi:10.1038/s41598-024-58204-6 · Cited by 9
Splice variants and regulatory networks associated with host resistance to the intestinal worm Cooperia oncophora in cattle
Li, R. W., Wu, S., Li, C., Li, W., & Schroeder, S. (2015) · Veterinary Parasitology · doi:10.1016/j.vetpar.2015.05.010 · Cited by 9
Transcriptome profiling of tolerogenic dendritic cells conditioned with dual mTOR kinase inhibitor, AZD8055
Shao, S., Cui, D., Ma, C., Chen, P., Zhou, B., Tao, R. N., & Wang, J. (2020) · International Immunopharmacology · doi:10.1016/j.intimp.2020.106241 · Cited by 9
Characterization of genetic variation and antioxidant properties in strawberry (Fragaria × ananassa Duch.) mutant genotypes
Ryu, J., Kim, W. J., Kim, S. H., Lee, K.-S., Jo, H.-J., Kim, E.-Y., Kim, S. H., Kang, S., Lee, J.-H., & Ha, B. (2020) · Genetic Resources and Crop Evolution · doi:10.1007/s10722-020-00918-3 · Cited by 9
Plastome phylogenomics and phylogenetic diversity of endangered and threatened grassland species (Poaceae) in a North American tallgrass prairie
Pischl, P. H., Burke, S. V., Bach, E. M., & Duvall, M. R. (2020) · Ecology and Evolution · doi:10.1002/ece3.6484 · Cited by 9
Map-based cloning identifies velvet A as a critical component of virulence in Fusarium pseudograminearum during infection of wheat heads
Gardiner, D. M., Rusu, A. G., Benfield, A. H., & Kazan, K. (2020) · Fungal Biology · doi:10.1016/j.funbio.2020.10.012 · Cited by 9
The microbial profile of a tissue necrosis affecting the Atlantic invasive coral Tubastraea tagusensis
Zanotti, A. A., Gregoracci, G. B., & Kitahara, M. V. (2021) · Scientific Reports · doi:10.1038/s41598-021-89296-z · Cited by 9
Inverted microbial community stratification and spatial–temporal stability in hypersaline anaerobic sediments from the S’Avall solar salterns
Font-Verdera, F., Liébana, R., Aldeguer‐Riquelme, B., Gangloff, V., Santos, F., Viver, T., & Rossello-Mora, R. A. (2021) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2021.126231 · Cited by 9
Incidence of RNA viruses infecting taro and tannia in East Africa and molecular characterisation of dasheen mosaic virus isolates
Kidanemariam, D., Sukal, A. C., Abraham, A. D., Njuguna, J. N., Stomeo, F., Dale, J. L., James, A. P., & Harding, R. M. (2021) · Annals of Applied Biology · doi:10.1111/aab.12725 · Cited by 9
MetaFunc: taxonomic and functional analyses of high throughput sequencing for microbiomes
Sulit, A. K., Kolisnik, T., Frizelle, F., Purcell, R. V., & Schmeier, S. (2023) · Gut Microbiome · doi:10.1017/gmb.2022.12 · Cited by 9
Genome sequence and comparative analysis of a Vibrio cholerae O139 strain E306 isolated from a cholera case in China
Yi, Y., Lü, N., Liu, F., Li, J., Zhang, R., Jia, L., Hua, J., Hu, X., Yang, Y., Zhu, B., et al. (2014) · Gut Pathogens · doi:10.1186/1757-4749-6-3 · Cited by 9
Microsatellite markers for the New Zealand endemic Myosotis pygmaea species group (Boraginaceae) amplify across species
Prebble, J. M., Tate, J. A., Meudt, H. M., & Symonds, V. V. (2015) · Applications in Plant Sciences · doi:10.3732/apps.1500027 · Cited by 9
Transcriptome-Based Identification of Differently Expressed Genes from Xanthomonas oryzae pv. oryzae Strains Exhibiting Different Virulence in Rice Varieties
Noh, T.-H., Song, E., Kim, H.-I., Kang, M.-H., & Park, Y. (2016) · International Journal of Molecular Sciences · doi:10.3390/ijms17020259 · Cited by 9
Screening potential SSR markers of the anadromous fish Coilia nasus by de novo transcriptome analysis using Illumina sequencing
Fang, D., Zhou, Y., Duan, J.-R., Zhang, M.-Y., Xu, D.-P., Liu, K., Xu, P., & Wei, Q. (2015) · Genetics and Molecular Research · doi:10.4238/2015.november.13.1 · Cited by 9
Computational problems of analysis of short next generation sequencing reads
Boekhorst, R. T., Naumenko, F. M., Orlova, N. G., Расимовна, Г. Э., Spitsina, A. M., Витальевна, Ч. И., Orlov, Y. L., & Abnizova, I. (2016) · Vavilov Journal of Genetics and Breeding · doi:10.18699/vj16.191 · Cited by 9
The finding of a new heterozygous mutation site of the SCN2A gene in a monozygotic twin family carrying and exhibiting genetic epilepsy with febrile seizures plus (GEFS+) using targeted next-generation sequencing
Liu, X., Li, W., Han, T., Wei, K., Qiao, S., Su, L., & Chi, Z. (2017) · Clinical Neurology and Neurosurgery · doi:10.1016/j.clineuro.2017.10.020 · Cited by 9
Bovine Genome Database: Tools for Mining the Bos taurus Genome
Hagen, D. E., Unni, D., Tayal, A., Burns, G. W., & Elsik, C. G. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7737-6_9 · Cited by 9
Draft Genome Sequence of Anaplasma marginale Strain Mex-01-001-01, a Mexican Strain That Causes Bovine Anaplasmosis
Quiroz-Castañeda, R. E., Amaro-Estrada, I., Martínez-Ocampo, F., Camarillo, S. D. R., Dantán‐González, E., Cobaxin-Cárdenas, M., & de la Torre, J. F. P. (2018) · Microbiology Resource Announcements · doi:10.1128/mra.01101-18 · Cited by 9
Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages
Gallo, G., Presta, L., Perrin, E., Gallo, M., Marchetto, D., Puglia, A. M., Fani, R., & Baldi, F. (2018) · BMC Microbiology · doi:10.1186/s12866-018-1330-5 · Cited by 9
Simultaneous profiling of Arabidopsis thaliana and Vibrio vulnificus MO6-24/O transcriptomes by dual RNA-seq analysis
Park, Y.-S., Park, J., Lee, S., Jung, S., Kim, S., & Ryu, C. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.04.008 · Cited by 10
Metagenomics and transcriptomics data from human colorectal cancer
Visnovska, T., Biggs, P. J., Schmeier, S., Frizelle, F., & Purcell, R. V. (2019) · Scientific Data · doi:10.1038/s41597-019-0117-3 · Cited by 9
Self-citation
Microbial Biomass in Mesophilic and Thermophilic High-Rate Biodigestion of Sugarcane Vinasse: Similar in Quantity, Different in Composition
Fuess, L. T., de Araújo, M. N., Saia, F. T., Gregoracci, G. B., Zaiat, M., & Lens, P. N. L. (2024) · Processes · doi:10.3390/pr12071356 · Cited by 8
A systematic survey of environmental DNA in Palau's lakes and waterfalls reveals an increase in Leptospira levels after flooding
Sato, Y., Tsurui‐Sato, K., Uchima, Y., Udui, C.-A., Lorin, O., Rengulbai, K., Toma, C., & Suzuki, R. (2024) · One Health · doi:10.1016/j.onehlt.2024.100898 · Cited by 9
Omnivorous Food Habits of the Endangered Ryukyu Long-Furred Rat Diplothrix legata (Muridae) Estimated Using the DNA Metabarcoding Method
Kobayashi, S., Sato, Y., & Izawa, M. (2024) · Mammal Study · doi:10.3106/ms2024-0007 · Cited by 8
Metagenomic surveillance reveals different structure and function of microbial community associated with mangrove pneumatophores and their surrounding matrices
Bohra, V., Lai, K. K.-Y., Lam, K.-L., Tam, N. F. Y., Xu, S. J., & Lee, F. W. F. (2025) · Marine Pollution Bulletin · doi:10.1016/j.marpolbul.2025.117614 · Cited by 8
A cost-effective barcode system for maize genetic discrimination based on bi-allelic InDel markers
Liang, S., Lin, F., Qian, Y., Zhang, T., Wu, Y., Qi, Y., Ren, S., Ruan, L., & Zhao, H. Q. (2020) · Plant Methods · doi:10.1186/s13007-020-00644-y · Cited by 8
Food safety assessment and toxicity study of the synbiotic consortium SBD111
Easson, D. D., Murphy, V. A., Ballok, A. E., Soto-Girón, M. J., Schott, E. M., Rodricks, J. V., & Toledo, G. V. (2022) · Food and Chemical Toxicology · doi:10.1016/j.fct.2022.113329 · Cited by 8
Characterization of Genes That Exhibit Genotype-Dependent Allele-Specific Expression and Its Implications for the Development of Maize Kernel
Dong, X., Luo, H., Yao, J., Guo, Q., Yu, S., Zhang, X., Cheng, X., & Meng, D. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24054766 · Cited by 8
The role of selenium intervention in gut microbiota homeostasis and gene function in mice with breast cancer on a high-fat diet
Li, Y., Liu, M., Kong, B., Zhang, G., & Zhang, Q. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1439652 · Cited by 8
A genetic linkage map of allo-octoploid strawberry (Fragaria × ananassa Duch.) using SNP markers
Lee, Y. R., & Lee, J. (2017) · Korean Journal of Breeding Science · doi:10.9787/kjbs.2017.49.3.119 · Cited by 8

Authors: Cox, M. P., Peterson, D. A., & Biggs, P. J.
Affiliations: Massey University (NZ)
Corresponding author: Cox, Murray P
ORCID: Cox, Murray P
Peterson, Daniel A
Biggs, Patrick J
Venue: BMC Bioinformatics
Publisher: Springer Science and Business Media LLC
Published: 2010-09-27
Volume: 11
Issue: 1
Pages: 485-485
ISSN: 1471-2105 (ISSN-L)
DOI: 10.1186/1471-2105-11-485
PMC: PMC2956736
OpenAlex: W2097205777
Cited by: 1,357
References: 9
Citations by year: 2026: 29 · 2025: 50 · 2024: 57 · 2023: 86 · 2022: 86 · 2021: 131 · 2020: 118 · 2019: 118 · 2018: 135 · 2017: 105 · 2016: 148 · 2015: 95 · 2014: 97 · 2013: 56 · 2012: 37
FWCI: 13.30
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/2.0 (tdm)
Locations: BMC Bioinformatics (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders: Royal Society
Royal Society Te Apārangi (MAU0802)
Massey University
Marsden Fund (MAU0802)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
Keywords: sequence trimming, quality control software
MeSH terms: Base Sequence, Software, Sequence Analysis, DNA, Sequence Analysis, RNA, Internet

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

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

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