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software:topical:lifescience:ngs_read_mapping_tools

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software:topical:lifescience:ngs_read_mapping_tools [2019/08/05 09:28]
meesters ["Standard Mappers"]
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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   * ''​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:​qc||quality check 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.1564990125.txt.gz · Last modified: 2019/08/05 09:28 by meesters