xander¶

Description¶

Xander Gene-targeted Metagenomic Assembler

Metagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. We present a novel method for targeting assembly of specific protein-coding genes using a graph structure combining both de Bruijn graphs and protein HMMs. The inclusion of HMM information guides the assembly, with concomitant gene annotation.

Environment Modules¶

Run module spider xander to find out what environment modules are available for this application.

Environment Variables¶

HPC_XANDER_DIR - installation directory
HPC_XANDER_BIN - executable directory
HPC_XANDER_DOC - documentation directory
HPC_XANDER_EXE - examples directory
HPC_XANDER_CONF - sample config directory

Configuration¶

Xander uses a configuration file which you must manually specify during your run. We provide a basic working configuration file at $HPC_XANDER_CONF/xander_setenv.sh. You must modify the SEQFILE and WORKDIR paths to your working directory.

$ml gcc/5.2.0 xander
$HPC_XANDER_CONF/xander_setenv.sh

Citation¶

If you publish research that uses xander you have to cite it as follows: [Wang, Q., J. A. Fish, M. Gilman, Y. Sun, C. T. Brown, J. M. Tiedje and J. R. Cole. Xander: Employing a Novel Method for Efficient Gene-Targeted Metagenomic Assembly. Microbiome.2015, 3:32. DOI: 10.1186/s40168-015-0093-6] (https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-015-0093-6)

Categories¶

biology, phylogenetics