Due to the complexity of the protocols and a limited knowledge of the nature of microbial communities, simulating metagenomic sequences plays an important role in testing the performance of existing tools and data analysis methods with metagenomic data. We developed metagenomic read simulators with platform-specific (Sanger, pyrosequencing, Illumina) base-error models, and simulated metagenomes of differing community complexities. We first evaluated the effect of rigorous quality control on Illumina data. Although quality filtering removed a large proportion of the data, it greatly improved the accuracy and contig lengths of resulting assemblies. We then compared the quality-trimmed Illumina assemblies to those from Sanger and pyrosequencing. For the simple community (10 genomes) all sequencing technologies assembled a similar amount and accurately represented the expected functional composition. For the more complex community (100 genomes) Illumina produced the best assemblies and more correctly resembled the expected functional composition. For the most complex community (400 genomes) there was very little assembly of reads from any sequencing technology. However, due to the longer read length the Sanger reads still represent...Continue Reading
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Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data
Reply to Delmont and Eren: Strain variants and population structure during the Deepwater Horizon oil spill
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Characterizing the fecal bacteria and archaea community of heifers and lactating cows through 16S rRNA next-generation sequencing
Information Theoretic Metagenome Assembly Allows the Discovery of Disease Biomarkers in Human Microbiome.
Metagenomic characterization of bacterial community and antibiotic resistance genes in representative ready-to-eat food in southern China
Metagenomic analysis for profiling of microbial communities and tolerance in metal-polluted pulp and paper industry wastewater.
Root microbiome assembly of As-hyperaccumulator Pteris vittata and its efficacy in arsenic requisition.
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