ArticleBioinformatics (Oxford, England)2011
Systematic exploration of error sources in pyrosequencing flowgram data.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Concordance between allele-specific PCR and ultra-deep pyrosequencing for the detection of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations.Journal of virological methods · 2014Trial
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- Rare deleterious germline variants and risk of lung cancer.NPJ precision oncology · 2021Article
- Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB).Journal of integrative bioinformatics · 2020Article
- Insights from the revised complete genome sequences ofMicrobial genomics · 2019Article
- Enhanced detection of microsatellite instability using pre-PCR elimination of wild-type DNA homo-polymers in tissue and liquid biopsies.Nucleic acids research · 2018Article
- Formal description of sequence-based voucherlessIMA fungus · 2018Article
- Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system.BMC genomics · 2018Article
- Diversity and Structure of Fungal Communities in Neotropical Rainforest Soils: The Effect of Host Recurrence.Microbial ecology · 2017Article
- MonoSeq Variant Caller Reveals Novel Mononucleotide Run Indel Mutations in Tumors with Defective DNA Mismatch Repair.Human mutation · 2016Article
- A comparison of tools for the simulation of genomic next-generation sequencing data.Nature reviews. Genetics · 2016Review
- RAS testing in metastatic colorectal cancer: advances in Europe.Virchows Archiv : an international journal of pathology · 2016Review
- Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies.Frontiers in microbiology · 2016Article
- A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding.Royal Society open science · 2016Article
- Species-wide genome sequence and nucleotide polymorphisms from the model allopolyploid plant Brassica napus.Scientific data · 2015Article
- Captured metagenomics: large-scale targeting of genes based on 'sequence capture' reveals functional diversity in soils.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Comparative genomics and experimental evolution of Escherichia coli BL21(DE3) strains reveal the landscape of toxicity escape from membrane protein overproduction.Scientific reports · 2015Article
- Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape.MicrobiologyOpen · 2015Article
- Mapping and determinism of soil microbial community distribution across an agricultural landscape.MicrobiologyOpen · 2015Article
- Draft Genome Sequence of Clostridium botulinum B2 450 Strain from Wound Botulism in a Drug User in Italy.Genome announcements · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivation454 pyrosequencing, by Roche Diagnostics, has emerged as an alternative to Sanger sequencing when it comes to read lengths, performance and cost, but shows higher per-base error rates. Although there are several tools available for noise removal, targeting different application fields, data interpretation would benefit from a better understanding of the different error types.
resultsBy exploring 454 raw data, we quantify to what extent different factors account for sequencing errors. In addition to the well-known homopolymer length inaccuracies, we have identified errors likely to originate from other stages of the sequencing process. We use our findings to extend the flowsim pipeline with functionalities to simulate these errors, and thus enable a more realistic simulation of 454 pyrosequencing data with flowsim. AVAILABILITY: The flowsim pipeline is freely available under the General Public License from http://biohaskell.org/Applications/FlowSim. CONTACT: susanne.balzer@imr.no.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.