Xander: employing a novel method for efficient gene-targeted metagenomic assembly.BACKGROUND
 Xander performs both assembly and annotation concomitantly using information incorporated in this graph.  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.  This method is implemented as open source software and is available at https://github.com/rdpstaff/Xander_assembler.
Xander
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. 
de Bruijn graph
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. 
protein profile hidden Markov model (HMM)
These are used to create a novel combined weighted assembly graph. 
combined weighted assembly 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. 
Human Microbiome Project (HMP)-defined community Illumina data