├── Contaminants └── contaminant_list.txt ├── Help ├── 1 Introduction │ └── 1.1 What is FastQC.html ├── 2 Basic Operations │ ├── 2.1 Opening a sequence file.html │ ├── 2.2 Evaluating Results.html │ └── 2.3 Saving a Report.html └── 3 Analysis Modules │ ├── 1 Basic Statistics.html │ ├── 10 Overrepresented Sequences.html │ ├── 11 Overrepresented Kmers.html │ ├── 2 Per Base Sequence Quality.html │ ├── 3 Per Sequence Quality Scores.html │ ├── 4 Per Base Sequence Content.html │ ├── 5 Per Base GC Content.html │ ├── 6 Per Sequence GC Content.html │ ├── 7 Per Base N Content.html │ ├── 8 Sequence Length Distribution.html │ ├── 9 Duplicate Sequences.html │ ├── duplication_levels.png │ ├── kmer_profiles.png │ ├── per_base_gc_content.png │ ├── per_base_n_content.png │ ├── per_base_quality.png │ ├── per_base_sequence_content.png │ ├── per_sequence_gc_content.png │ ├── per_sequence_quality.png │ └── sequence_length_distribution.png ├── INSTALL.txt ├── LICENSE.txt ├── README.md ├── README.txt ├── RELEASE_NOTES.txt ├── Templates ├── Icons │ ├── error.png │ ├── fastqc_icon.png │ ├── tick.png │ └── warning.png └── header_template.html ├── fastqc ├── fastqc-csf ├── Contaminants │ └── contaminant_list.txt ├── INSTALL.txt ├── LICENSE.txt ├── README.md ├── README.txt ├── RELEASE_NOTES.txt ├── build.xml ├── fastqc ├── fastqc_icon.ico └── run_fastqc.bat ├── fastqc_icon.ico ├── jbzip2-0.9.jar ├── run_fastqc.bat ├── sam-1.32.jar └── uk └── ac └── bbsrc └── babraham └── FastQC ├── Analysis ├── AnalysisListener.java ├── AnalysisQueue.java ├── AnalysisRunner.java └── OfflineRunner.java ├── Dialogs ├── AboutDialog.java ├── FastQCTitlePanel.java └── WelcomePanel.java ├── FastQCApplication.java ├── FastQCMenuBar.java ├── FileFilters ├── BAMFileFilter.java ├── CasavaFastQFileFilter.java ├── FastQFileFilter.java ├── GobyFileFilter.java ├── MappedBAMFileFilter.java └── SequenceFileFilter.java ├── Graphs ├── BaseGroup.java ├── LineGraph.java └── QualityBoxPlot.java ├── Help ├── HelpDialog.java ├── HelpIndexRoot.java ├── HelpPage.java ├── HelpPageDisplay.java └── HelpSearchPanel.java ├── Modules ├── BasicStats.java ├── DuplicationLevel.java ├── GCModel │ ├── GCModel.java │ └── GCModelValue.java ├── KmerContent.java ├── NContent.java ├── OverRepresentedSeqs.java ├── PerBaseGCContent.java ├── PerBaseQualityScores.java ├── PerBaseSequenceContent.java ├── PerSequenceGCContent.java ├── PerSequenceQualityScores.java ├── QCModule.java └── SequenceLengthDistribution.java ├── Report ├── HTMLReportArchive.java └── stylesheet.txt ├── Resources ├── error.png ├── fastqc_icon.png ├── fastqc_icon.svg ├── fastqc_icon_100.png ├── tick.png └── warning.png ├── Results └── ResultsPanel.java ├── Sequence ├── BAMFile.java ├── Contaminant │ ├── Contaminant.java │ ├── ContaminantHit.java │ └── ContaminentFinder.java ├── FastQFile.java ├── GobyFile.java ├── QualityEncoding │ └── PhredEncoding.java ├── Sequence.java ├── SequenceFactory.java ├── SequenceFile.java ├── SequenceFileGroup.java └── 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