Difference between revisions of "Xander"

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m (Text replacement - "#uppercase" to "uc")
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==System Variables==
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{#uppercase:{{#var:app}}}}_CONF - base configuration file directory
* HPC_{{uc:{{#var:app}}}}_CONF - base configuration file directory
{{#if: {{#var: conf}}|==Configuration==
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 21:29, 6 December 2019


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


  • gcc/5.2.0
  • xander

System Variables

  • HPC_XANDER_DIR - installation directory
  • HPC_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


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.