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software:topical:lifescience:ngs_read_mapping_tools [2019/07/29 16:42]
meesters
software:topical:lifescience:ngs_read_mapping_tools [2019/10/24 15:48] (current)
meesters [BarraCuda]
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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/​SeqAn/<​version>''​ ''​bio/​SeqAn/<​version>''​
  
-You can find a wrapper to ease your workflow, [[software:​topical:​lifescience:#​standard_mappers|below]], eventually ((not yet)).+You can find a wrapper to ease your workflow, [[software:​topical:​lifescience:#​standard_mappers|below]].
  
  
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 Module(s) can be found at: Module(s) can be found at:
  
-''​bio/​STAR/<​version>''​+''​bio/​Bowtie2/<​version>''​ 
 + 
 +You can find a wrapper to ease your workflow, [[software:​topical:​lifescience:#​standard_mappers|below]].
  
 ==== STAR ==== ==== STAR ====
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 ''​bio/​STAR/<​version>''​ ''​bio/​STAR/<​version>''​
 +
 +You can find a wrapper to ease your workflow, [[software:​topical:​lifescience:#​standard_mappers|below]].
  
 ==== segemehl ==== ==== segemehl ====
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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]].
  
  
software/topical/lifescience/ngs_read_mapping_tools.1564411329.txt.gz · Last modified: 2019/07/29 16:42 by meesters