Difference between revisions of "Metaxa2"

Latest revision as of 19:29, 18 August 2022

Description

Metaxa2 is a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets.

Environment Modules

Run module spider metaxa2 to find out what environment modules are available for this application.

System Variables

HPC_METAXA2_DIR - installation directory

Citation

If you publish research that uses metaxa2 you have to cite it as follows:

Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2: Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data. Molecular Ecology Resources (2015). doi: 10.1111/1755-0998.12399

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Biology]][[Category:NGS]]
+[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:sequencing]]
 {|<!--CONFIGURATION: REQUIRED-->
-|{{#vardefine:app|Metaxa2}}
+|{{#vardefine:app|metaxa2}}
-|{{#vardefine:url|}}
+|{{#vardefine:url|http://microbiology.se/software/metaxa2/}}
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
@@ Line 10: / Line 10: @@
 |{{#vardefine:testing|}}       <!--PROFILING-->
 |{{#vardefine:faq|}}             <!--FAQ-->
-|{{#vardefine:citation|}}       <!--CITATION-->
+|{{#vardefine:citation|1}}       <!--CITATION-->
 |{{#vardefine:installation|}} <!--INSTALLATION-->
 |}
@@ Line 21: / Line 21: @@
 <!--Modules-->
-==Required Modules==
+==Environment Modules==
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-===Serial===
-* {{#var:app}}
-<!--
-===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 69: / Line 58: @@
 If you publish research that uses {{#var:app}} you have to cite it as follows:
-WRITE_CITATION_HERE
+[http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12399/abstract Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2: Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data. Molecular Ecology Resources (2015). doi: 10.1111/1755-0998.12399]
 |}}
 <!--Installation-->