Sha256: b8c09825a588d130bf21d4a550b7f4ef1509efe322ff12973537f721572163c2
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Size: 1.6 KB
Versions: 10
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Stored size: 1.6 KB
Contents
# ====================================== # 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>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,PluginFindPolyAt,PluginAbAdapters,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 adapters_ab_db="adapters_illumina.fasta"
Version data entries
10 entries across 10 versions & 1 rubygems