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

# Help: <br/>This template is used to preprocess short reads for genomics including low complexity removal<br/> # Help: <br/>Plugin list and aplication order:<br/>

# Help: <ul> # Help: <li>PluginIndeterminations: retaining the longest sequence fragment without indeterminations (N)</li> # Help: <li>PluginAbAdapters: trimming the Illumina 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: <li>PluginLowComplexity: sequences with low complexity are stored on a separate file. </li> # Help: </ul>

plugin_list = PluginIndeterminations,PluginAbAdapters,PluginUserContaminants,PluginContaminants,PluginVectors,PluginLowQuality,PluginLowComplexity

generate_initial_stats = false

# Minimum insert size for every trimmed sequence

min_insert_size_trimmed = 30

# do not remove cloned sequences remove_clonality=false

adapters_ab_db=“adapters_illumina.fasta”