Corpus ID: 14913979

Illumina Sequencing Artifacts Revealed by Connectivity Analysis of Metagenomic Datasets

@article{Howe2012IlluminaSA,
  title={Illumina Sequencing Artifacts Revealed by Connectivity Analysis of Metagenomic Datasets},
  author={Adina Howe and Jason Pell and Rosangela Canino-Koning and Rachel Mackelprang and Susannah G. Tringe and Janet K. Jansson and James M. Tiedje and C. Titus Brown},
  journal={arXiv: Genomics},
  year={2012}
}
Sequencing errors and biases in metagenomic datasets affect coverage-based assemblies and are often ignored during analysis. Here, we analyze read connectivity in metagenomes and identify the presence of problematic and likely a-biological connectivity within metagenome assembly graphs. Specifically, we identify highly connected sequences which join a large proportion of reads within each real metagenome. These sequences show position-specific bias in shotgun reads, suggestive of sequencing… Expand
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References

SHOWING 1-10 OF 30 REFERENCES
Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
TLDR
This research developed metagenomic read simulators with platform-specific (Sanger, pyrosequencing, Illumina) base-error models, and simulated metagenomes of differing community complexities, and examined the effect of rigorous quality control on Illumina data. Expand
Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data
TLDR
A critical assessment of current de novo short reads assembly tools in multi-genome scenarios using complex simulated metagenomic data and shows that the assembly process reduces the accuracy of the functional classification of the metagenomics data and that these errors can be overcome raising the coverage of the studied metagenome. Expand
Assembly algorithms for next-generation sequencing data.
TLDR
This review summarizes and compares the published descriptions of packages named SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo to compare the two standard methods known as the de Bruijn graph approach and the overlap/layout/consensus approach to assembly. Expand
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
TLDR
MetaVelvet succeeded to generate higher N50 scores and smaller chimeric scaffolds than any compared single-genome assemblers, produce high-quality scaffolds as well as the separate assembly using Velvet from isolated species sequence reads, and MetaVelvet reconstructed even relatively low-coverage genome sequences as scaffolds. Expand
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
TLDR
Three simulated data sets were designed to model real metagenomes in terms of complexity and phylogenetic composition and explored the effects of the simulated community structure and method combinations on the fidelity of each processing step by comparison to the corresponding isolate genomes. Expand
A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE
TLDR
This work presents DRISEE as an open-source, platform-independent method to assess sequencing error in shotgun metagenomic data, and utilizes it to discover previously uncharacterized error in de novo sequence data from the 454 and Illumina sequencing platforms. Expand
Genome assembly reborn: recent computational challenges
  • M. Pop
  • Medicine, Computer Science
  • Briefings Bioinform.
  • 2009
TLDR
The major algorithmic approaches for genome assembly are outlined and recent developments in this domain are described. Expand
De novo assembly of human genomes with massively parallel short read sequencing.
TLDR
The development of this de novo short read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way. Expand
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs
TLDR
A memory-efficient graph representation based on a probabilistic data structure, a Bloom filter, that allows us to efficiently store assembly graphs in as little as 4 bits per k-mer, albeit inexactly, is introduced, which reduces the overall memory requirements for de novo assembly of metagenomes. Expand
Systematic artifacts in metagenomes from complex microbial communities
TLDR
A systematic error is found in metagenomes generated by 454-based pyrosequencing that leads to an overestimation of gene and taxon abundance; between 11% and 35% of sequences in a typical metagenome are artificial replicates. Expand
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