# ======================================
# General parameters GENOMICS WITH POSSIBLE LINKER
# ======================================

# Help: <br/>This template is used to preprocess Roche 454 genomic data <br/>

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

# 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>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 = PluginLowHighSize,PluginMids,PluginIndeterminations,PluginAbAdapters,PluginUserContaminants,PluginContaminants,PluginVectors,PluginLowQuality