Characteristics of 454 pyrosequencing data--enabling realistic simulation with flowsim
نویسندگان
چکیده
منابع مشابه
Filtering duplicate reads from 454 pyrosequencing data
MOTIVATION Throughout the recent years, 454 pyrosequencing has emerged as an efficient alternative to traditional Sanger sequencing and is widely used in both de novo whole-genome sequencing and metagenomics. Especially the latter application is extremely sensitive to sequencing errors and artificially duplicated reads. Both are common in 454 pyrosequencing and can create a strong bias in the e...
متن کاملSystematic exploration of error sources in pyrosequencing flowgram data
MOTIVATION 454 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. RESUL...
متن کاملCritique: ”Filtering duplicate reads from 454 pyrosequencing”
The paper describes a novel approach for filtering duplicate reads from 454 pyrosequencing data. This problem is motivated by the need of reduce sequencing errors and artifically duplicated reads in some applications such as de-novo whole genome sequencing or metagenomics. Existing solutions are often based on nucleotide sequences, while raw flowgram values, which contain additional information...
متن کاملQuantifying microbial communities with 454 pyrosequencing: does read abundance count?
Pyrosequencing technologies have revolutionized how we describe and compare complex microbial communities. In 454 pyrosequencing data sets, the abundance of reads pertaining to taxa or phylotypes is commonly interpreted as a measure of genic or taxon abundance, useful for quantitative comparisons of community similarity. Potentially systematic biases inherent in sample processing, amplification...
متن کاملEvaluating Characteristics of De Novo Assembly Software on 454 Transcriptome Data: A Simulation Approach
BACKGROUND The quantity of transcriptome data is rapidly increasing for non-model organisms. As sequencing technology advances, focus shifts towards solving bioinformatic challenges, of which sequence read assembly is the first task. Recent studies have compared the performance of different software to establish a best practice for transcriptome assembly. Here, we adapted a simulation approach ...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2010
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btq365