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 accessAbstract
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.
Overview
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
Cites
Statistics
Figures
![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.](/paper-figures/c7aa17d75a5648cb9be4d664599fd049/pandaseq-paired-end-assembler-for-illumina-sequences-figure-4.jpg)
Verification
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?
In the citing paper
“However, it assumes that all paired-end reads can be merged.”
From PEAR: a fast and accurate Illumina Paired-End reAd mergeR (2014) · cites this paper as Masella et al., 2012
In the citing paper
“PANDAseq merges fragments by maximizing the probability of true sequence matches, given the observed sequences.”
From PEAR: a fast and accurate Illumina Paired-End reAd mergeR (2014) · cites this paper as Masella et al., 2012
In the citing paper
“It combines quality scores with sequence matches and thereby improves merging quality.”
From PEAR: a fast and accurate Illumina Paired-End reAd mergeR (2014) · cites this paper as Masella et al., 2012
In the citing paper
“In contrast to FLASH, PANDAseq works well with short overlap regions and does not require prior knowledge of the target DNA fragment size.”
From PEAR: a fast and accurate Illumina Paired-End reAd mergeR (2014) · cites this paper as Masella et al., 2012
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
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
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
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
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-citationIllumina-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
Research works printed but not linked: 1
- Illumina, Inc: CASAVA Software Version 1.7 User Guide. Illumina, Inc; 2010.
Cited by
Sorted by citations
Items 1,001–1,002 of 1,002
Kim, M. C., Lee, S., Park, J. K., Park, J., Lee, D., Park, J., Kim, B.-Y., Cho, M. S., Kim, T.-Y., Park, H. Y., et al. (2021) · Journal of Medicinal Food · doi:10.1089/jmf.2020.4746 · Cited by 18
Deciphering Trifolium pratense L. holobiont reveals a microbiome resilient to future climate changes
Wahdan, S. F. M., Tanunchai, B., Wu, Y., Sansupa, C., Schädler, M., Dawoud, T. M., Buscot, F., & Purahong, W. (2021) · MicrobiologyOpen · doi:10.1002/mbo3.1217 · Cited by 15
Metadata
- 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
- Venue
- BMC Bioinformatics
- Published
- 2012-02-14
- Volume
- 13
- Issue
- 1
- Pages
- 31-31
- ISSN
- 1471-2105 (ISSN-L)
- 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
