# ====================================== # General parameters to extract Amplicons # ======================================
# Help: <br/>This template is used to get Amplicons<br/>
# Help: <br/>Plugin list and aplication order:<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 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>PluginAmplicons: getting sequences contained between two primers. Sequences with less than two primers are rejected. </li> # Help: <li>PluginLowQuality: trimming low quality regions from sequences. </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