[FastQC]
Per base sequence quality = per_base_quality.png
Per sequence quality scores = per_sequence_quality.png
Per base sequence content = per_base_sequence_content.png
Per base GC content = per_base_gc_content.png
Per sequence GC content = per_sequence_gc_content.png
Per base N content = per_base_n_content.png
Sequence Length Distribution= sequence_length_distribution.png
Sequence Duplication Levels = duplication_levels.png
Kmer Content = kmer_profiles.png
Per tile sequence quality = per_tile_quality.png
Adapter Content = adapter_content.png

[Trimmomatic]
illuminaClip_seedMismatch = 2
illuminaClip_simpleClip = 10
leading = 3
trailing = 3
trimOption = SLIDINGWINDOW:4:20
trimBetter_threshold = 0.15

[forAssembly.Illumina]
trimBetter_threshold = 0.1
trimOption = SLIDINGWINDOW:4:25

[forAssembly.IonTorrent]
trimBetter_threshold = 0.2
trimOption = SLIDINGWINDOW:4:15

[forMapping.Illumina]
trimBetter_threshold = 0.15
trimOption = SLIDINGWINDOW:4:15

[forMapping.IonTorrent]
trimBetter_threshold = 0.25
trimOption = SLIDINGWINDOW:4:15

[Fileextension]
fastq = .fastq.gz, .fastq, .fq, .fq.gz
bam = .bam

[Pattern]
sep=_
R1 = R1
R2 = R2
lane = L\d{3}