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software:topical:lifescience:qc

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software:topical:lifescience:qc [2019/01/28 14:16]
meesters [The Wrapper Module on Mogon]
software:topical:lifescience:qc [2019/01/28 15:44] (current)
meesters [The Wrapper Module on Mogon]
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 Within the specified (or default) output directory, you will find back your sample subdirectories (if any were present. The prefix of each sample is preserved. As the wrapper allows only certain designators to distinguish the mate pairs (see the limitations,​ above), these are also preserved. Trimmomatic splits it output in reads which are paired and unpaired (if any). The later are written in a subdirectory ''​unpaired''​ as of version ''​0.2''​. Within the specified (or default) output directory, you will find back your sample subdirectories (if any were present. The prefix of each sample is preserved. As the wrapper allows only certain designators to distinguish the mate pairs (see the limitations,​ above), these are also preserved. Trimmomatic splits it output in reads which are paired and unpaired (if any). The later are written in a subdirectory ''​unpaired''​ as of version ''​0.2''​.
 +
 +==== Selecting the Executable ====
 +
 +<WRAP center round todo 60%>
 +Note: The figure below is not the final evaluation - this is forthcoming. I assume that the assumption will hold, that flexbar outperform trimmomatic.
 +</​WRAP>​
 +
 +{{:​software:​topical:​lifescience:​speed_trimming.png?​direct&​400 |}} Selecting the executable should consider the following 3 minimum criteria:
 +  - Speed as indicated in the left figure
 +  - The memory footprint, which is negligible except for trimmomatic,​ where on Mogon II a higher reservation,​ than the default memory was necessary to implement.
 +  - Quality. Here, flexbar is the most feature rich, but also the most complex.
 +
software/topical/lifescience/qc.txt · Last modified: 2019/01/28 15:44 by meesters