Inferring viral quasispecies spectra from 454 pyrosequencing reads
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 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...
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This paper addresses the problem of reconstructing viral quasispecies from next-generation sequencing reads obtained from amplicons (i.e., reads generated from predefined amplified overlapping regions). We compare the parsimonious and likelihood models for this problem and propose several novel assembling algorithms. The proposed methods have been validated on simulated error-free HCV and real ...
متن کامل454-Pyrosequencing: A Molecular Battiscope for Freshwater Viral Ecology
Viruses, the most abundant biological entities on the planet, are capable of infecting organisms from all three branches of life, although the majority infect bacteria where the greatest degree of cellular diversity lies. However, the characterization and assessment of viral diversity in natural environments is only beginning to become a possibility. Through the development of a novel technique...
متن کاملAggressive assembly of pyrosequencing reads with mates
MOTIVATION DNA sequence reads from Sanger and pyrosequencing platforms differ in cost, accuracy, typical coverage, average read length and the variety of available paired-end protocols. Both read types can complement one another in a 'hybrid' approach to whole-genome shotgun sequencing projects, but assembly software must be modified to accommodate their different characteristics. This is true ...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2011
ISSN: 1471-2105
DOI: 10.1186/1471-2105-12-s6-s1