Meta-IDBA: a de Novo assembler for metagenomic data

By Yu Peng, Henry C. M. Leung, Siu Ming Yiu, Francis Y. L. Chin. Bioinform., 2011

333 citations recorded by the source corpus.

Motivation: Next-generation sequencing techniques allow us to generate reads from a microbial environment in order to analyze the microbial community. However, assembling of a set of mixed reads from different species to form contigs is a bottleneck of metagenomic research. Although there are many assemblers for assembling reads from a single genome, there are no assemblers for assembling reads in metagenomic data without reference genome sequences. Moreover, the performances of these assemblers on metagenomic data are far from satisfactory, because of the existence of common regions in the genomes of subspecies and species, which make the assembly problem much more complicated. Results: We introduce the Meta-IDBA algorithm for assembling reads in metagenomic data, which contain multiple genomes from different species. There are two core steps in Meta-IDBA. It first tries to partition the de Bruijn graph into isolated components of different species based on an important observation. Then, for each component, it captures the slight variants of the genomes of subspecies from the same species by multiple alignments and represents the genome of one species, using a consensus sequence. Comparison of the performances of Meta-IDBA and existing assemblers, such as Velvet and Abyss for different metagenomic datasets shows that Meta-IDBA can reconstruct longer contigs with similar accuracy. Availability: Meta-IDBA toolkit is available at our website http://www.cs.hku.hk/~alse/metaidba. Contact: chin@cs.hku.hk

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ccd2dfbcc8c5e415c1a5401ddabe7d873d8a2dbc

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Citations in the corpus

Computational meta'omics for microbial community studies (2013, background): “Only a subset of these includes MetaVelvet (Namiki et al , 2012), khmer (Pell et al , 2012), metAMOS (Treangen et al , 2011b), Meta-IDBA (Peng et al , 2011), and MetaORFA (Ye and Tang, 2009).”
Next-Generation Sequencing Technology: Current Trends and Advancements (2023, background): “However, a close monitoring and comprehensive understanding of the host–microbiome and microbiome–intercommunity interactions are vital to healthy survival.”
Applications of next-generation sequencing to the study of biological invasions (2015, background): “Furthermore, it is possible to simultaneously sequence genomes of different species, such as the metagenomic sequencing (i.e. the study of many genomes) of microbial communities (Laserson et al., 2011; Peng et al., 2011).”
metaSPAdes: a new versatile metagenomic assembler. (2017, methodology): “SRX024329) generated by the the Human Microbiome Project (Huttenhower et al. 2012) that was used for benchmarking in Peng et al. (2011); Treangen et al. (2013); Mikheenko et al. (2016).”
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth (2012, methodology): “Results on existing general purpose assemblers like Velvet (Zerbino and Birney, 2008), SOAPdenovo (Li et al., 2010), IDBA (Peng et al., 2010) and special purpose assemblers like Velvet-SC (Chitsaz et al., 2011), Meta-IDBA (Peng et al., 2011) were compared.”