ArticleBMC genomics2011
Evaluation of short read metagenomic assembly.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Article
- Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences.Briefings in bioinformatics · 2020Review
- Evaluating the Performance of De Novo Assembly Methods for Venom-Gland Transcriptomics.Toxins · 2018Article
- Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix NThe New phytologist · 2018Article
- Statistical correction for functional metagenomic profiling of a microbial community with short NGS reads.Journal of applied statistics · 2018Article
- Assembling metagenomes, one community at a time.BMC genomics · 2017Article
- Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics.PloS one · 2017Article
- Translational metagenomics and the human resistome: confronting the menace of the new millennium.Journal of molecular medicine (Berlin, Germany) · 2017Review
- Review
- Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia.Applied and environmental microbiology · 2016Article
- InteMAP: Integrated metagenomic assembly pipeline for NGS short reads.BMC bioinformatics · 2015Article
- Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities.BMC genomics · 2015Article
- Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages.Frontiers in microbiology · 2015Article
- VTBuilder: a tool for the assembly of multi isoform transcriptomes.BMC bioinformatics · 2014Article
- Evaluation of viral genome assembly and diversity estimation in deep metagenomes.BMC genomics · 2014Article
- Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation.BMC genomics · 2014Article
- Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut.BMC genomics · 2014Article
- New approaches indicate constant viral diversity despite shifts in assemblage structure in an Australian hypersaline lake.Applied and environmental microbiology · 2013Article
- Sequence assembly demystified.Nature reviews. Genetics · 2013Review
- Next-generation sequence assembly: four stages of data processing and computational challenges.PLoS computational biology · 2013Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMetagenomic assembly is a challenging problem due to the presence of genetic material from multiple organisms. The problem becomes even more difficult when short reads produced by next generation sequencing technologies are used. Although whole genome assemblers are not designed to assemble metagenomic samples, they are being used for metagenomics due to the lack of assemblers capable of dealing with metagenomic samples. We present an evaluation of assembly of simulated short-read metagenomic samples using a state-of-art de Bruijn graph based assembler.
resultsWe assembled simulated metagenomic reads from datasets of various complexities using a state-of-art de Bruijn graph based parallel assembler. We have also studied the effect of k-mer size used in de Bruijn graph on metagenomic assembly and developed a clustering solution to pool the contigs obtained from different assembly runs, which allowed us to obtain longer contigs. We have also assessed the degree of chimericity of the assembled contigs using an entropy/impurity metric and compared the metagenomic assemblies to assemblies of isolated individual source genomes.
conclusionsOur results show that accuracy of the assembled contigs was better than expected for the metagenomic samples with a few dominant organisms and was especially poor in samples containing many closely related strains. Clustering contigs from different k-mer parameter of the de Bruijn graph allowed us to obtain longer contigs, however the clustering resulted in accumulation of erroneous contigs thus increasing the error rate in clustered contigs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.