Difference between revisions of "Xander"
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_CONF - base configuration file directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 21:29, 6 December 2019
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.
Required Modules
Serial
- 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
Citation
If you publish research that uses xander you have to cite it as follows: