Difference between revisions of "AdapterRemoval"
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Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BiologyCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|adapterremoval}} |{{#vardefine:url|https://github.com/MikkelSchube...") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Phylogenetics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|adapterremoval}} | |{{#vardefine:app|adapterremoval}} | ||
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|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|[http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-016-1900-2 Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88]}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | + | [http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-016-1900-2 Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88] | |
|}} | |}} | ||
Latest revision as of 20:47, 11 August 2022
Description
This program searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, the AdapterRemoval may be used to recover a consensus adapter sequence for paired-ended data, for which this information is not available.
Environment Modules
Run module spider adapterremoval to find out what environment modules are available for this application.
System Variables
- HPC_ADAPTERREMOVAL_DIR - installation directory
- HPC_ADAPTERREMOVAL_BIN - executable directory
Citation
If you publish research that uses adapterremoval you have to cite it as follows: