# ======================================
# General parameters to extract Amplicons
# ======================================

# Help: <br/>This template is used to get Amplicons<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>PluginKey: trimming Roche 454 sequencing keys (typically 4 first nucleotides)</li>
# Help: <li>PluginMids: trimming Roche 454 MIDs</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>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>PluginFindPolyAt: trimming PolyA and PolyT. After a PolyT, the sequence is checked for low complexity. </li>
# Help: <li>PluginAmplicons: getting sequences contained between two primers. Sequences with less than two primers are rejected. </li>
# Help: <li>PluginLinker: splits Roche 454 paired-end sequences by any linker found in linkers database. Linker is removed.</li>
# Help: <li>PluginLowComplexity: sequences with low complexity are stored on a separate file. </li>
# Help: <li>PluginLowQuality: trimming low quality regions from sequences. </li>
# Help: <li>PluginVectors: trimming any cloning vector found in SeqTrimNEXT database. </li>
# Help: </ul>

plugin_list = PluginLowHighSize,PluginKey,PluginMids,PluginIndeterminations,PluginAbAdapters,PluginAmplicons,PluginLowQuality

# do not remove cloned sequences
remove_clonality=false

# sequences containing with diferent keys (barcodes) are saved to separate folders
use_independent_folder_for_each_key=true

# remove amplicons containing less or equal number of sequences indicated

minimal_repetitions_for_amplicons=1