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# General parameters TRANSCRIPTOMICS PLANTS
# ======================================

# Help: <br/>This template is used to preprocess Roche 454 transcriptomic data. Customized for plants.<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>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 cont_mitochondrias.fasta cont_plastids.fasta"


# do not remove cloned sequences
remove_clonality=true