Sha256: fbc99cb2b226b08f722449feb34ebd19fe4e96871404a5a20531a6941c61a339
Contents?: true
Size: 1.4 KB
Versions: 10
Compression:
Stored size: 1.4 KB
Contents
# ============================================================== # General parameters for genomics - Illumina/SOLiD (short reads) # ============================================================== # Help: <br/>This template is used to preprocess short reads for genomics <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>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: </ul> plugin_list = PluginIndeterminations,PluginAbAdapters,PluginUserContaminants,PluginContaminants,PluginVectors,PluginLowQuality generate_initial_stats = false # Minimum insert size for every trimmed sequence min_insert_size_trimmed = 30 min_quality=20 min_insert_size_trimmed=40 min_insert_size_paired=40 # do not remove cloned sequences remove_clonality=false adapters_ab_db="adapters_illumina.fasta"
Version data entries
10 entries across 10 versions & 1 rubygems