transcriptomics_454.txt in seqtrimnext-2.0.52

- old
+ new
@@ -2,9 +2,26 @@
 # General parameters TRANSCRIPTOMICS 
 # ======================================
 
 # Help: <br/>This template is used to preprocess Roche 454 transcriptomic data <br/>
 
+# Help: <br/><b>Plugin list and aplication order:</b><br/>
 
-plugin_list = PluginLowHighSize,PluginMids,PluginIndeterminations,PluginAbAdapters,PluginAdapters,PluginFindPolyAt,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity
+# Help: <ul>
+# Help: <li>PluginLowHighSize: rejecting too short or too long sequences</li>
+# Help: <li>PluginMids: trimming Roche 454 MIDs and keys</li>
+# Help: <li>PluginIndeterminations: retaining the longest sequence fragment without indeterminations (N)</li>
+# Help: <li>PluginAbAdapters: trimming the Roche 454 AB adapters</li>
+# Help: <li>PluginAdapters: trimming the adapters found in SeqTrimNEXT database</li>
+# Help: <li>PluginFindPolyAt: trimming PolyA and PolyT. After a PolyT, the sequence is checked for low complexity. </li>
+
+# Help: <li>PluginUserContaminants: discarding sequences matching any entry in the user contaminant database saving them in a separate file</li>
+
+# Help: <li>PluginContaminants: trimming the contaminant fragments found in the contaminant database. When contamination is prevalent, sequences are rejected. </li>
+# Help: <li>PluginVectors: trimming any cloning vector found in SeqTrimNEXT database. </li>
+# Help: <li>PluginLowQuality: trimming low quality regions from sequences. </li>
+# Help: <li>PluginLowComplexity: sequences with low complexity are stored on a separate file. </li>
+# Help: </ul>
+
+plugin_list = PluginLowHighSize,PluginMids,PluginIndeterminations,PluginAbAdapters,PluginAdapters,PluginFindPolyAt,PluginUserContaminants,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity
 
 contaminants_db="contaminants.fasta cont_ribosome.fasta"