title: Xander: employing a novel method for efficient gene-targeted metagenomic assembly.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, MI USA.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, MI USA ; Department of Computer Science and Engineering, Michigan State University, East Lansing, MI USA.
authors.forename: Jordan A
authors.initials: JA
authors.lastname: Fish
authors.affiliation: Department of Computer Science and Engineering, Michigan State University, East Lansing, MI USA.
authors.forename: Mariah
authors.initials: M
authors.lastname: Gilman
authors.affiliation: Department of Computer Science and Engineering, Michigan State University, East Lansing, MI USA.
authors.forename: Yanni
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Department of Computer Science and Engineering, Michigan State University, East Lansing, MI USA ; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA.
authors.forename: C Titus
authors.initials: CT
authors.lastname: Brown
authors.affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, MI USA ; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA ; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI USA.
authors.forename: James M
authors.initials: JM
authors.lastname: Tiedje
authors.affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, MI USA ; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI USA.
authors.forename: James R
authors.initials: JR
authors.lastname: Cole
keywords: Assembly; Biofuel crop; Functional gene; HMM; Metagenomics; Nitrogen cycle; nifH; nirK