# ======================================
# General parameters for transcriptomics - Illumina/SOLiD (short reads)
# ======================================

# Help: <br/>This template is used to preprocess short reads for transcriptomics<br/>
# Help: <br/><b>Plugin list and aplication order:</b><br/>

# Help: <ul>
# Help: <li>PluginIndeterminations: retaining the longest sequence fragment without indeterminations (N)</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 = PluginIndeterminations,PluginFindPolyAt,PluginUserContaminants,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity

contaminants_db="contaminants.fasta cont_ribosome.fasta"

generate_initial_stats = false

# Minimum insert size for every trimmed sequence

min_insert_size_trimmed = 30

# do not remove cloned sequences
remove_clonality=false