Difference between revisions of "Xander"
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| + | * HPC_{{uc:{{#var:app}}}}_CONF - base configuration file directory | ||
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{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | Configuration File | + | '''Configuration File''' |
| − | Xander 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. | + | |
| + | 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 | $ ml gcc/5.2.0 xander | ||
Latest revision as of 19:07, 10 June 2022
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.
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: