Xander

Description

xander website  

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.

Required Modules

Serial

• gcc/5.2.0
• xander

System Variables

• HPC_{{#uppercase:xander}}_DIR - installation directory
• HPC_{{#uppercase:xander}}_CONF - base configuration file directory

Additional Information

Configuration File

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.