Short Barcodes for Next Generation Sequencing

Mir, Katharina; Neuhaus, Klaus; Bossert, Martin; Schober, Steffen

doi:10.1371/journal.pone.0082933

Cited by 19 publications

(14 citation statements)

References 15 publications

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“…To sequence large numbers of samples in parallel, short nucleotide barcodes (usually between 6-12 nucleotides) are developed, evaluated, and applied to multiplex samples on different NGS platforms (Mir et al 2013;Parameswaran et al 2007; Bartram et al 2011;Smith et al 2010;Hamady et al 2008). For pyrosequencing, lists of 1,544 errorcorrecting forward barcodes and 48 forward-reverse barcode pairs (10-base) were provided in publications of Hamady et al (2008) and Parameswaran et al (2007), respectively.…”

Section: S Rrna Gene High-throughput Sequencingmentioning

confidence: 99%

Application of Metagenomics in Environmental Anaerobic Technology

Ju¹,

Fang²,

Zhang³

2015

Anaerobic Biotechnology

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Anaerobic technology has been applied for the treatment of solid wastes and wastewater since the 1880s. This chapter reviews the most recent advance in molecular microbial characterization techniques, i.e., metagenomics, as well as its applications in anaerobic technology, from the exploration of the intriguing science of anaerobes to industrial engineering applications. With the rapidly decreasing cost of high-throughput sequencing technologies and timely updating of state-of-the-art bioinformatics analysis tools, metagenomics has revolutionized the study of microbiology and demonstrated the great potential of the development of novel microbial resources (e.g., industrial biomolecules and enzymes and biodegradation genes), as it discloses unprecedented genetic information of uncultivated microorganisms at an amazingly fast rate. This chapter gives a detailed introduction to the technical procedures of metagenomics, from preliminary molecular experiments to high-throughput sequencing, as well as its application in environmental anaerobic technology.

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Section: S Rrna Gene High-throughput Sequencingmentioning

confidence: 99%

Application of Metagenomics in Environmental Anaerobic Technology

Ju¹,

Fang²,

Zhang³

2015

Anaerobic Biotechnology

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“…Adapter parts might be erroneously sequenced in the beginning of a read, and thus may introduce artificial mutations [35][36][37]. There are a number of popular tools for adaptor removing from raw sequence reads [34,[38][39][40].…”

Section: Box 3: Base Calls Their Qualities and Readsmentioning

confidence: 99%

“…In pooled multiplex sequencing, the size of each pool is a critical issue [38,39]. Thus reasonably even dimultiplexing [20,35,40] ensures less biased data.…”

Section: Box 3: Base Calls Their Qualities and Readsmentioning

confidence: 99%

Computational Errors and Biases in Short Read Next Generation Sequencing

Abnizova¹,

Boekhorst²,

Orlov³

2017

J Proteomics Bioinform

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“…Pheniqs offers two demultiplexing strategies: the traditional minimum distance decoder, previously described in detail in the context of sequencing (Mir et al, 2013), and a novel Phred-adjusted maximum likelihood decoder that not only outperforms the former but also consults base calling quality scores and reports a decoding error probability. The minimum distance decoder bundled with Pheniqs can produce results identical to traditional demultiplexers and relies on the minimal pairwise mismatch distance between the barcode sequences (defined as the number of corresponding positions with non-identical bases) to provide a worst-case scenario estimate for an unambiguous error correction threshold (Shannon, 1948).…”

Section: Approachmentioning

confidence: 99%

Pheniqs: Fast and flexible quality-aware sequence demultiplexing

Galanti

Shasha

Gunsalus

2017

Preprint

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Motivation: Output from high throughput sequencing instruments often exceeds what is necessary to assay a single sample. To better utilize this capacity, multiple samples are independently tagged with a unique "barcode" sequence and are then pooled, or "multiplexed", and sequenced together. Classifying, or "demultiplexing", the reads involves decoding the barcode sequence.Although instruments estimate the probability of incorrectly calling each nucleobase, available demultiplexers do not consult those estimates or report classification error probabilities. Results: We present Pheniqs, a fast and flexible sequence demultiplexer and quality analyzer. In addition to providing an efficient implementation of the widespread minimum distance decoder, Pheniqs introduces a novel Phred-adjusted maximum likelihood decoder that consults base calling quality scores and estimates the probability of a barcode decoding error. Setting an upper bound on the permissible error provides an intuitive way to control demultiplexing confidence and directly influence precision and recall. Pheniqs supports FASTQ and multiple Sequence Alignment/Map formats and uses auxiliary SAM tags to report both library classification and demultiplexing error probability. Evaluation on both real and semi-synthetic data indicates that Pheniqs is faster than existing demultiplexers, substantially when demultiplexing longer reads, and achieves greater accuracy by correctly reflecting quality measurements. Availability and Implementation: Implemented in multithreaded C++ and available under the terms of the AGPL-3.0 license agreement at

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Short Barcodes for Next Generation Sequencing

Cited by 19 publications

References 15 publications

Application of Metagenomics in Environmental Anaerobic Technology

Application of Metagenomics in Environmental Anaerobic Technology

Computational Errors and Biases in Short Read Next Generation Sequencing

Pheniqs: Fast and flexible quality-aware sequence demultiplexing

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