software:topical:lifescience:ngs_read_mapping_tools

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Last revision Both sides next revision
software:topical:lifescience:ngs_read_mapping_tools [2019/07/29 16:42]
meesters
software:topical:lifescience:ngs_read_mapping_tools [2019/08/05 09:29]
meesters fix: broken link
Line 31: Line 31:
 ''​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]].
  
  
Line 40: Line 40:
 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 ====
Line 49: Line 51:
  
 ''​bio/​STAR/<​version>''​ ''​bio/​STAR/<​version>''​
 +
 +You can find a wrapper to ease your workflow, [[software:​topical:​lifescience:#​standard_mappers|below]].
  
 ==== segemehl ==== ==== segemehl ====
Line 62: Line 66:
 ''​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 ====
  
Line 109: Line 125:
  
   * ''​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:
Line 174: Line 190:
 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.txt
  • Last modified: 2019/10/24 15:48
  • by meesters