software:topical:lifescience:ngs_read_mapping_tools

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software:topical:lifescience:ngs_read_mapping_tools [2019/07/29 16:43]
meesters
software:topical:lifescience:ngs_read_mapping_tools [2020/10/02 14:52]
jrutte02 removed
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 See [[:software:topical:lifescience:ngs_read_mapping_tools#gpu-based|below for a wrapper script]] to ease your workflow. See [[:software:topical:lifescience:ngs_read_mapping_tools#gpu-based|below for a wrapper script]] to ease your workflow.
 +
 +==== Minimap2 ====
 +
 +[[https://github.com/lh3/minimap2|Minimap2]] is supposed to be a replacement for ''bwa mem''. Modules are installed under 
 +
 +''bio/minimap2''
  
  
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 ''bio/segemehl/0.2.0-foss-2018a'' ''bio/segemehl/0.2.0-foss-2018a''
  
 +==== TopHat ====
 +
 +[[https://ccb.jhu.edu/software/tophat/index.shtml|TopHat]] is a fast splice junction mapper for RNA-Seq reads.
 +
 +Module can be found at:
 +
 +''bio/TopHat/<version>''
 +
 +
 +<WRAP center round info 90%>
 +This program is not yet incorporated into the wrapping module.
 +</WRAP>
 ==== yara ==== ==== yara ====
  
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   * ''referencedir'' needs to be the (relative) path to a directory containing an indexed BWA reference   * ''referencedir'' needs to be the (relative) path to a directory containing an indexed BWA reference
-  * ''inputdir'' needs to be a (relative) path to a directory containing all inputs. Subdirectories and files containing the string ''unpaired'' are ignored; this is to support preprocessing with the [[software:topical:lifescience:trimmomatic|trimmomatic module]].+  * ''inputdir'' needs to be a (relative) path to a directory containing all inputs. Subdirectories and files containing the string ''unpaired'' are ignored; this is to support preprocessing with the [[software:topical:lifescience:qc|quality check module]].
  
 The options: The options:
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 About Arguments: About Arguments:
   * ''referencedir'' needs to be the (relative) path to a directory containing an indexed BWA reference. No symbolic links are allowed.   * ''referencedir'' needs to be the (relative) path to a directory containing an indexed BWA reference. No symbolic links are allowed.
-  * ''inputdir'' needs to be a (relative) path to a directory containing all inputs. Subdirectories and files containing the string ''unpaired'' are ignored; this is to support preprocessing with the [[software:topical:lifescience:trimmomatic|trimmomatic module]].+  * ''inputdir'' needs to be a (relative) path to a directory containing all inputs. Subdirectories and files containing the string ''unpaired'' are ignored; this is to support preprocessing with the [[software:topical:lifescience:qc|quality check module]].