Xander: employing a novel method for efficient gene-targeted metagenomic assembly

Metagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. Current methods often assemble only fragmented partial genes. We present a novel method for targeting assembly of specific protein-coding gene...

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Bibliographic Details
Published in:Microbiome 2015-08, Vol.3 (1), p.32-32, Article 32
Main Authors: Wang, Qiong, Fish, Jordan A, Gilman, Mariah, Sun, Yanni, Brown, C Titus, Tiedje, James M, Cole, James R
Format: Article
Language:English
Subjects:
Analysis
Assembly
BASIC BIOLOGICAL SCIENCES
Biofuel crop
Functional gene
Genes
HMM
Markov processes
Metagenomics
Methods
nifH
nirK
Nitrogen cycle
Phylogeny
Public software
Software
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Summary:Metagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. Current methods often assemble only fragmented partial genes. We present a novel method for targeting assembly of specific protein-coding genes. This method combines a de Bruijn graph, as used in standard assembly approaches, and a protein profile hidden Markov model (HMM) for the gene of interest, as used in standard annotation approaches. These are used to create a novel combined weighted assembly graph. Xander performs both assembly and annotation concomitantly using information incorporated in this graph. We demonstrate the utility of this approach by assembling contigs for one phylogenetic marker gene and for two functional marker genes, first on Human Microbiome Project (HMP)-defined community Illumina data and then on 21 rhizosphere soil metagenomic datasets from three different crops totaling over 800 Gbp of unassembled data. We compared our method to a recently published bulk metagenome assembly method and a recently published gene-targeted assembler and found our method produced more, longer, and higher quality gene sequences. Xander combines gene assignment with the rapid assembly of full-length or near full-length functional genes from metagenomic data without requiring bulk assembly or post-processing to find genes of interest. HMMs used for assembly can be tailored to the targeted genes, allowing flexibility to improve annotation over generic annotation pipelines. This method is implemented as open source software and is available at https://github.com/rdpstaff/Xander_assembler.
ISSN:2049-2618
2049-2618
DOI:10.1186/s40168-015-0093-6