# ====================================== # General parameters SANGER # ======================================

# Help: <br/>This template is used to preprocess Sanger genomic data <br/>

# Help: <br/>Plugin list and aplication order:<br/>

# Help: <ul> # Help: <li>PluginIndeterminations: retaining the longest sequence fragment without indeterminations (N)</li> # Help: <li>PluginAdapters: trimming adapters</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: </ul>

plugin_list = PluginIndeterminations,PluginSangerAdapters,PluginFindPolyAt,PluginContaminants,PluginVectors,PluginLowQuality

# do not remove cloned sequences remove_clonality=false