├── LICENSE ├── README.md ├── archs4 ├── .htaccess ├── archs4zoo.html ├── buildExpressionMatrix.r ├── css │ ├── animate.css │ ├── bootstrap.min.css │ ├── bootstrap.tables.css │ ├── css.css │ ├── desert.css │ ├── dropzone.css │ ├── easy-autocomplete.min.css │ ├── easy-autocomplete.themes.min.css │ ├── footer.css │ ├── jquery-ui.css │ ├── jquery.auto-complete.css │ ├── main.css │ ├── menu-vertical.css │ ├── selectize.css │ ├── spectrum.css │ └── styles.css ├── data.html ├── data │ ├── gene_human_tsne.csv │ ├── gene_mouse_tsne.csv │ ├── sample_human_tsne.csv │ └── sample_mouse_tsne.csv ├── download.html ├── help.html ├── images │ ├── ARCHS-04.png │ ├── archs-42.png │ ├── archs-icon.png │ ├── archs-icon2.png │ ├── archs4zoo.png │ ├── arrow.png │ ├── atom.png │ ├── biojupies.png │ ├── biorxiv.png │ ├── congruent_pentagon.png │ ├── congruent_pentagon2.png │ ├── correlation.png │ ├── createfile.gif │ ├── dcic.png │ ├── dnaicon2.png │ ├── enrichment.png │ ├── enrichr-icon.png │ ├── enrichr.png │ ├── genesearch.png │ ├── human_foot.png │ ├── human_foot_small.png │ ├── human_foot_small_white.png │ ├── json.png │ ├── labflask.png │ ├── metasearch.png │ ├── mountsinai.png │ ├── mouse_foot.png │ ├── mouse_foot_small.png │ ├── mouse_foot_small_white.png │ ├── naturecomm.png │ ├── pipeline.png │ ├── pipeline2.png │ ├── prediction.png │ ├── r.png │ ├── remove.png │ ├── results.png │ ├── sampleicon2.png │ ├── selection.png │ ├── sigsearch.png │ ├── tissue.png │ ├── twitter.png │ ├── viewer.png │ └── viewoption.png ├── index.html ├── scripts │ ├── .Rhistory │ ├── bootstrap.js │ ├── clipboard.min.js │ ├── cloud.min.js │ ├── control.js │ ├── d3.layout.cloud.js │ ├── dropzone.js │ ├── getSimilarGene.php │ ├── jquery-3.1.1.min.js │ ├── jquery.2.min.js │ ├── jquery.auto-complete.min.js │ ├── jquery.easy-autocomplete.min.js │ ├── jquery.sticky.js │ ├── logic.js │ ├── marquee.js │ ├── menu-vertical.js │ ├── orbitcontrols.js │ ├── prettify.js │ ├── saveSvgAsPng.js │ ├── search.js │ ├── selectize.js │ ├── spectrum.js │ ├── tags.js │ ├── three.min.js │ └── word-cloud.js ├── search │ ├── dataStats.php │ ├── dbconfig.php │ ├── downloadtracker.php │ ├── emaillist.php │ ├── genepage.php │ ├── getGSEmatrix.php │ ├── getGenes.php │ ├── getSampleMatch.php │ ├── getSeriesMatch.php │ ├── getSeriesMetadata.php │ ├── getSeriesView.php │ ├── loadExpressionTissue.php │ ├── loadenrichment.php │ ├── receivesimilarity.php │ ├── searchEnrichmentGenes.php │ ├── searchEnrichmentSamples.php │ ├── series.php │ ├── seriespage.html │ ├── seriespage.php │ ├── test.php │ └── userstat.php └── tabs │ ├── searchenrichment.html │ ├── searchgenes.html │ ├── searchmeta.html │ └── searchsignature.html ├── docker ├── awskallisto │ ├── DockerKallisto │ ├── buildContainers.sh │ ├── deployStar.json │ ├── scripts │ │ ├── allAlign.py │ │ ├── autostartKallisto.sh │ │ ├── fastqc.sh │ │ ├── genelevel.r │ │ ├── runKallisto.sh │ │ ├── sendcounts.pl │ │ └── sradump.sh │ └── tools │ │ ├── fastqc │ │ ├── Configuration │ │ │ ├── adapter_list.txt │ │ │ ├── contaminant_list.txt │ │ │ └── limits.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 Adapter Content.html │ │ │ │ ├── 11 Kmer Content.html │ │ │ │ ├── 12 Per Tile Sequence Quality.html │ │ │ │ ├── 2 Per Base Sequence Quality.html │ │ │ │ ├── 3 Per Sequence Quality Scores.html │ │ │ │ ├── 4 Per Base Sequence Content.html │ │ │ │ ├── 5 Per Sequence GC Content.html │ │ │ │ ├── 6 Per Base N Content.html │ │ │ │ ├── 7 Sequence Length Distribution.html │ │ │ │ ├── 8 Duplicate Sequences.html │ │ │ │ ├── 9 Overrepresented 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 │ │ │ │ ├── per_tile_quality.png │ │ │ │ └── sequence_length_distribution.png │ │ ├── INSTALL.txt │ │ ├── LICENSE.txt │ │ ├── LICENSE_JHDF5.txt │ │ ├── README.txt │ │ ├── RELEASE_NOTES.txt │ │ ├── Templates │ │ │ ├── Icons │ │ │ │ ├── error.png │ │ │ │ ├── fastqc_icon.png │ │ │ │ ├── tick.png │ │ │ │ └── warning.png │ │ │ ├── fastqc2fo.xsl │ │ │ └── header_template.html │ │ ├── cisd-jhdf5.jar │ │ ├── fastqc │ │ ├── fastqc_icon.ico │ │ ├── jbzip2-0.9.jar │ │ ├── net │ │ │ └── sourceforge │ │ │ │ └── iharder │ │ │ │ └── base64 │ │ │ │ ├── Base64$1.class │ │ │ │ ├── Base64$InputStream.class │ │ │ │ ├── Base64$OutputStream.class │ │ │ │ └── Base64.class │ │ ├── org │ │ │ └── apache │ │ │ │ └── commons │ │ │ │ └── math3 │ │ │ │ ├── analysis │ │ │ │ ├── UnivariateFunction.class │ │ │ │ └── solvers │ │ │ │ │ ├── AbstractUnivariateSolver.class │ │ │ │ │ ├── AllowedSolution.class │ │ │ │ │ ├── BaseAbstractUnivariateSolver.class │ │ │ │ │ ├── BaseUnivariateSolver.class │ │ │ │ │ ├── BracketedUnivariateSolver.class │ │ │ │ │ ├── BrentSolver.class │ │ │ │ │ ├── UnivariateSolver.class │ │ │ │ │ └── UnivariateSolverUtils.class │ │ │ │ ├── distribution │ │ │ │ ├── AbstractIntegerDistribution.class │ │ │ │ ├── AbstractRealDistribution$1.class │ │ │ │ ├── AbstractRealDistribution.class │ │ │ │ ├── BetaDistribution.class │ │ │ │ ├── BinomialDistribution.class │ │ │ │ ├── CauchyDistribution.class │ │ │ │ ├── ChiSquaredDistribution.class │ │ │ │ ├── FDistribution.class │ │ │ │ ├── GammaDistribution.class │ │ │ │ ├── HypergeometricDistribution.class │ │ │ │ ├── IntegerDistribution.class │ │ │ │ ├── NormalDistribution.class │ │ │ │ ├── PascalDistribution.class │ │ │ │ ├── PoissonDistribution.class │ │ │ │ ├── RealDistribution.class │ │ │ │ ├── SaddlePointExpansion.class │ │ │ │ ├── TDistribution.class │ │ │ │ ├── WeibullDistribution.class │ │ │ │ └── ZipfDistribution.class │ │ │ │ ├── exception │ │ │ │ ├── ConvergenceException.class │ │ │ │ ├── DimensionMismatchException.class │ │ │ │ ├── MathArithmeticException.class │ │ │ │ ├── MathIllegalArgumentException.class │ │ │ │ ├── MathIllegalNumberException.class │ │ │ │ ├── MathIllegalStateException.class │ │ │ │ ├── MathInternalError.class │ │ │ │ ├── MaxCountExceededException.class │ │ │ │ ├── NoBracketingException.class │ │ │ │ ├── NotFiniteNumberException.class │ │ │ │ ├── NotPositiveException.class │ │ │ │ ├── NotStrictlyPositiveException.class │ │ │ │ ├── NullArgumentException.class │ │ │ │ ├── NumberIsTooLargeException.class │ │ │ │ ├── NumberIsTooSmallException.class │ │ │ │ ├── OutOfRangeException.class │ │ │ │ ├── TooManyEvaluationsException.class │ │ │ │ └── util │ │ │ │ │ ├── ArgUtils.class │ │ │ │ │ ├── ExceptionContext.class │ │ │ │ │ ├── ExceptionContextProvider.class │ │ │ │ │ ├── Localizable.class │ │ │ │ │ └── LocalizedFormats.class │ │ │ │ ├── random │ │ │ │ ├── AbstractWell.class │ │ │ │ ├── BitsStreamGenerator.class │ │ │ │ ├── RandomData.class │ │ │ │ ├── RandomDataImpl.class │ │ │ │ ├── RandomGenerator.class │ │ │ │ └── Well19937c.class │ │ │ │ ├── special │ │ │ │ ├── Beta$1.class │ │ │ │ ├── Beta.class │ │ │ │ ├── Erf.class │ │ │ │ ├── Gamma$1.class │ │ │ │ └── Gamma.class │ │ │ │ └── util │ │ │ │ ├── ArithmeticUtils.class │ │ │ │ ├── ContinuedFraction.class │ │ │ │ ├── DoubleArray.class │ │ │ │ ├── FastMath$ExpFracTable.class │ │ │ │ ├── FastMath$ExpIntTable.class │ │ │ │ ├── FastMath$lnMant.class │ │ │ │ ├── FastMath.class │ │ │ │ ├── FastMathCalc.class │ │ │ │ ├── FastMathLiteralArrays.class │ │ │ │ ├── Incrementor$1.class │ │ │ │ ├── Incrementor$MaxCountExceededCallback.class │ │ │ │ ├── Incrementor.class │ │ │ │ ├── MathUtils.class │ │ │ │ ├── Precision.class │ │ │ │ └── ResizableDoubleArray.class │ │ ├── run_fastqc.bat │ │ ├── sam-1.103.jar │ │ └── uk │ │ │ └── ac │ │ │ └── babraham │ │ │ └── FastQC │ │ │ ├── Analysis │ │ │ ├── AnalysisListener.class │ │ │ ├── AnalysisQueue.class │ │ │ ├── AnalysisRunner.class │ │ │ └── OfflineRunner.class │ │ │ ├── Dialogs │ │ │ ├── AboutDialog$1.class │ │ │ ├── AboutDialog.class │ │ │ ├── FastQCTitlePanel$SmoothJLabel.class │ │ │ ├── FastQCTitlePanel.class │ │ │ └── WelcomePanel.class │ │ │ ├── FastQCApplication$1.class │ │ │ ├── FastQCApplication.class │ │ │ ├── FastQCConfig.class │ │ │ ├── FastQCMenuBar.class │ │ │ ├── FileFilters │ │ │ ├── BAMFileFilter.class │ │ │ ├── CasavaFastQFileFilter.class │ │ │ ├── FastQFileFilter.class │ │ │ ├── GobyFileFilter.class │ │ │ ├── MappedBAMFileFilter.class │ │ │ └── SequenceFileFilter.class │ │ │ ├── Graphs │ │ │ ├── BaseGroup.class │ │ │ ├── LineGraph.class │ │ │ ├── QualityBoxPlot.class │ │ │ └── TileGraph.class │ │ │ ├── Help │ │ │ ├── HelpDialog.class │ │ │ ├── HelpIndexRoot$FileSorter.class │ │ │ ├── HelpIndexRoot.class │ │ │ ├── HelpPage.class │ │ │ ├── HelpPageDisplay$HelpEditor.class │ │ │ ├── HelpPageDisplay.class │ │ │ └── HelpSearchPanel.class │ │ │ ├── Modules │ │ │ ├── AbstractQCModule.class │ │ │ ├── AdapterContent$Adapter.class │ │ │ ├── AdapterContent$ResultsTable.class │ │ │ ├── AdapterContent.class │ │ │ ├── BasicStats$ResultsTable.class │ │ │ ├── BasicStats.class │ │ │ ├── DuplicationLevel.class │ │ │ ├── GCModel │ │ │ │ ├── GCModel.class │ │ │ │ └── GCModelValue.class │ │ │ ├── KmerContent$Kmer.class │ │ │ ├── KmerContent$ResultsTable.class │ │ │ ├── KmerContent.class │ │ │ ├── ModuleConfig.class │ │ │ ├── ModuleFactory.class │ │ │ ├── NContent.class │ │ │ ├── OverRepresentedSeqs$OverrepresentedSeq.class │ │ │ ├── OverRepresentedSeqs$ResultsTable.class │ │ │ ├── OverRepresentedSeqs.class │ │ │ ├── PerBaseQualityScores.class │ │ │ ├── PerBaseSequenceContent.class │ │ │ ├── PerSequenceGCContent.class │ │ │ ├── PerSequenceQualityScores.class │ │ │ ├── PerTileQualityScores.class │ │ │ ├── QCModule.class │ │ │ └── SequenceLengthDistribution.class │ │ │ ├── Report │ │ │ ├── HTMLReportArchive.class │ │ │ └── stylesheet.txt │ │ │ ├── Resources │ │ │ ├── error.png │ │ │ ├── fastqc_icon.png │ │ │ ├── fastqc_icon.svg │ │ │ ├── fastqc_icon_100.png │ │ │ ├── tick.png │ │ │ └── warning.png │ │ │ ├── Results │ │ │ ├── ResultsPanel$ModuleRenderer.class │ │ │ └── ResultsPanel.class │ │ │ ├── Sequence │ │ │ ├── BAMFile.class │ │ │ ├── Contaminant │ │ │ │ ├── Contaminant.class │ │ │ │ ├── ContaminantHit.class │ │ │ │ └── ContaminentFinder.class │ │ │ ├── Fast5File.class │ │ │ ├── FastQFile.class │ │ │ ├── QualityEncoding │ │ │ │ └── PhredEncoding.class │ │ │ ├── Sequence.class │ │ │ ├── SequenceFactory.class │ │ │ ├── SequenceFile.class │ │ │ ├── SequenceFileGroup.class │ │ │ └── SequenceFormatException.class │ │ │ ├── Statistics │ │ │ ├── NormalDistribution.class │ │ │ └── PearsonCorrelation.class │ │ │ └── Utilities │ │ │ ├── CasavaBasename.class │ │ │ ├── HotColdColourGradient.class │ │ │ ├── ImageToBase64.class │ │ │ ├── MultiMemberGZIPInputStream.class │ │ │ ├── NameFormatException.class │ │ │ ├── NanoporeBasename.class │ │ │ ├── QualityCount.class │ │ │ └── RGB.class │ │ ├── kallisto │ │ ├── README.md │ │ ├── kallisto │ │ ├── license.txt │ │ └── test │ │ │ ├── README.md │ │ │ ├── Snakefile │ │ │ ├── ind │ │ │ ├── kallisto_bin_Debug_0.42.4 │ │ │ ├── out │ │ │ ├── abundance.h5 │ │ │ ├── abundance.tsv │ │ │ └── run_info.json │ │ │ ├── reads_1.fastq.gz │ │ │ ├── reads_2.fastq.gz │ │ │ └── transcripts.fasta.gz │ │ └── sratools │ │ └── bin │ │ ├── fastdump │ │ ├── fastdump.2 │ │ ├── fastdump.2.8.2 │ │ ├── fastq-dump │ │ ├── fastq-dump.2 │ │ └── fastq-dump.2.8.2 ├── awsscheduler │ ├── .idea │ │ ├── jsLibraryMappings.xml │ │ ├── mint.iml │ │ ├── misc.xml │ │ ├── modules.xml │ │ ├── runConfigurations │ │ │ └── bin_www.xml │ │ └── workspace.xml │ ├── DockerfileScheduler │ ├── buildContainers.sh │ ├── marathon.json │ └── upload │ │ ├── .idea │ │ ├── copyright │ │ │ └── profiles_settings.xml │ │ ├── misc.xml │ │ ├── modules.xml │ │ ├── php.xml │ │ ├── upload.iml │ │ └── workspace.xml │ │ ├── buildExpressionMatrix.r │ │ ├── css │ │ ├── bootstrap.min.css │ │ ├── bootstrap.tables.css │ │ ├── desert.css │ │ ├── dropzone.css │ │ ├── footer.css │ │ ├── jquery-ui.css │ │ ├── main.css │ │ ├── spectrum.css │ │ └── styles.css │ │ ├── data │ │ └── autoCompleteList.json │ │ ├── dbconfig.php │ │ ├── getjob.php │ │ ├── images │ │ ├── ARCHS-04.png │ │ ├── arc.png │ │ ├── arc_icon.png │ │ ├── archs-icon2.png │ │ ├── armadillo.png │ │ ├── armadilloglow.png │ │ ├── armadillorainbow.png │ │ ├── armadillorainbowsmall.png │ │ ├── atom.png │ │ ├── dna.png │ │ ├── facebook.png │ │ ├── favicon-16x16.png │ │ ├── favicon-32x32.png │ │ ├── favicon.ico │ │ ├── google-plus.png │ │ ├── human_foot.png │ │ ├── human_foot_small.png │ │ ├── human_foot_small_white.png │ │ ├── linkedin.png │ │ ├── mouse-312012_960_720.png │ │ ├── mouse_foot.png │ │ ├── mouse_foot_small.png │ │ ├── mouse_foot_small_white.png │ │ ├── mouseicon.png │ │ ├── psi_icon.png │ │ ├── psi_large.png │ │ ├── psi_small.png │ │ ├── psi_text.png │ │ ├── remove.png │ │ └── twitter.png │ │ ├── index.html │ │ ├── index.php │ │ ├── listfiles.php │ │ ├── sampledata.php │ │ ├── scripts │ │ ├── bootstrap.js │ │ ├── clipboard.min.js │ │ ├── cloud.min.js │ │ ├── control.js │ │ ├── d3.layout.cloud.js │ │ ├── dropzone.js │ │ ├── jquery-3.1.1.min.js │ │ ├── jquery.2.min.js │ │ ├── logic.js │ │ ├── prettify.js │ │ ├── rook.r │ │ ├── search.js │ │ ├── spectrum.js │ │ ├── tags.js │ │ ├── three.min.js │ │ └── word-cloud.js │ │ ├── upload.php │ │ ├── uploadS3.py │ │ ├── uploadgenecount.php │ │ ├── waiting.php │ │ ├── webgl.html │ │ └── webgl.php └── awsstar │ ├── DockerStar │ ├── buildContainers.sh │ ├── deployStar.json │ ├── scripts │ ├── allAlign.py │ ├── autostartStar.sh │ ├── fastqc.sh │ ├── genelevel.r │ ├── parseGTF.r │ ├── runKallisto.sh │ ├── sendcounts.pl │ └── sradump.sh │ └── tools │ ├── fastqc │ ├── Configuration │ │ ├── adapter_list.txt │ │ ├── contaminant_list.txt │ │ └── limits.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 Adapter Content.html │ │ │ ├── 11 Kmer Content.html │ │ │ ├── 12 Per Tile Sequence Quality.html │ │ │ ├── 2 Per Base Sequence Quality.html │ │ │ ├── 3 Per Sequence Quality Scores.html │ │ │ ├── 4 Per Base Sequence Content.html │ │ │ ├── 5 Per Sequence GC Content.html │ │ │ ├── 6 Per Base N Content.html │ │ │ ├── 7 Sequence Length Distribution.html │ │ │ ├── 8 Duplicate Sequences.html │ │ │ ├── 9 Overrepresented 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 │ │ │ ├── per_tile_quality.png │ │ │ └── sequence_length_distribution.png │ ├── INSTALL.txt │ ├── LICENSE.txt │ ├── LICENSE_JHDF5.txt │ ├── README.txt │ ├── RELEASE_NOTES.txt │ ├── Templates │ │ ├── Icons │ │ │ ├── error.png │ │ │ ├── fastqc_icon.png │ │ │ ├── tick.png │ │ │ └── warning.png │ │ ├── fastqc2fo.xsl │ │ └── header_template.html │ ├── cisd-jhdf5.jar │ ├── fastqc │ ├── fastqc_icon.ico │ ├── jbzip2-0.9.jar │ ├── net │ │ └── sourceforge │ │ │ └── iharder │ │ │ └── base64 │ │ │ ├── Base64$1.class │ │ │ ├── Base64$InputStream.class │ │ │ ├── Base64$OutputStream.class │ │ │ └── Base64.class │ ├── org │ │ └── apache │ │ │ └── commons │ │ │ └── math3 │ │ │ ├── analysis │ │ │ ├── UnivariateFunction.class │ │ │ └── solvers │ │ │ │ ├── AbstractUnivariateSolver.class │ │ │ │ ├── AllowedSolution.class │ │ │ │ ├── BaseAbstractUnivariateSolver.class │ │ │ │ ├── BaseUnivariateSolver.class │ │ │ │ ├── BracketedUnivariateSolver.class │ │ │ │ ├── BrentSolver.class │ │ │ │ ├── UnivariateSolver.class │ │ │ │ └── UnivariateSolverUtils.class │ │ │ ├── distribution │ │ │ ├── AbstractIntegerDistribution.class │ │ │ ├── AbstractRealDistribution$1.class │ │ │ ├── AbstractRealDistribution.class │ │ │ ├── BetaDistribution.class │ │ │ ├── BinomialDistribution.class │ │ │ ├── CauchyDistribution.class │ │ │ ├── ChiSquaredDistribution.class │ │ │ ├── FDistribution.class │ │ │ ├── GammaDistribution.class │ │ │ ├── HypergeometricDistribution.class │ │ │ ├── IntegerDistribution.class │ │ │ ├── NormalDistribution.class │ │ │ ├── PascalDistribution.class │ │ │ ├── PoissonDistribution.class │ │ │ ├── RealDistribution.class │ │ │ ├── SaddlePointExpansion.class │ │ │ ├── TDistribution.class │ │ │ ├── WeibullDistribution.class │ │ │ └── ZipfDistribution.class │ │ │ ├── exception │ │ │ ├── ConvergenceException.class │ │ │ ├── DimensionMismatchException.class │ │ │ ├── MathArithmeticException.class │ │ │ ├── MathIllegalArgumentException.class │ │ │ ├── MathIllegalNumberException.class │ │ │ ├── MathIllegalStateException.class │ │ │ ├── MathInternalError.class │ │ │ ├── MaxCountExceededException.class │ │ │ ├── NoBracketingException.class │ │ │ ├── NotFiniteNumberException.class │ │ │ ├── NotPositiveException.class │ │ │ ├── NotStrictlyPositiveException.class │ │ │ ├── NullArgumentException.class │ │ │ ├── NumberIsTooLargeException.class │ │ │ ├── NumberIsTooSmallException.class │ │ │ ├── OutOfRangeException.class │ │ │ ├── TooManyEvaluationsException.class │ │ │ └── util │ │ │ │ ├── ArgUtils.class │ │ │ │ ├── ExceptionContext.class │ │ │ │ ├── ExceptionContextProvider.class │ │ │ │ ├── Localizable.class │ │ │ │ └── LocalizedFormats.class │ │ │ ├── random │ │ │ ├── AbstractWell.class │ │ │ ├── BitsStreamGenerator.class │ │ │ ├── RandomData.class │ │ │ ├── RandomDataImpl.class │ │ │ ├── RandomGenerator.class │ │ │ └── Well19937c.class │ │ │ ├── special │ │ │ ├── Beta$1.class │ │ │ ├── Beta.class │ │ │ ├── Erf.class │ │ │ ├── Gamma$1.class │ │ │ └── Gamma.class │ │ │ └── util │ │ │ ├── ArithmeticUtils.class │ │ │ ├── ContinuedFraction.class │ │ │ ├── DoubleArray.class │ │ │ ├── FastMath$ExpFracTable.class │ │ │ ├── FastMath$ExpIntTable.class │ │ │ ├── FastMath$lnMant.class │ │ │ ├── FastMath.class │ │ │ ├── FastMathCalc.class │ │ │ ├── FastMathLiteralArrays.class │ │ │ ├── Incrementor$1.class │ │ │ ├── Incrementor$MaxCountExceededCallback.class │ │ │ ├── Incrementor.class │ │ │ ├── MathUtils.class │ │ │ ├── Precision.class │ │ │ └── ResizableDoubleArray.class │ ├── run_fastqc.bat │ ├── sam-1.103.jar │ └── uk │ │ └── ac │ │ └── babraham │ │ └── FastQC │ │ ├── Analysis │ │ ├── AnalysisListener.class │ │ ├── AnalysisQueue.class │ │ ├── AnalysisRunner.class │ │ └── OfflineRunner.class │ │ ├── Dialogs │ │ ├── AboutDialog$1.class │ │ ├── AboutDialog.class │ │ ├── FastQCTitlePanel$SmoothJLabel.class │ │ ├── FastQCTitlePanel.class │ │ └── WelcomePanel.class │ │ ├── FastQCApplication$1.class │ │ ├── FastQCApplication.class │ │ ├── FastQCConfig.class │ │ ├── FastQCMenuBar.class │ │ ├── FileFilters │ │ ├── BAMFileFilter.class │ │ ├── CasavaFastQFileFilter.class │ │ ├── FastQFileFilter.class │ │ ├── GobyFileFilter.class │ │ ├── MappedBAMFileFilter.class │ │ └── SequenceFileFilter.class │ │ ├── Graphs │ │ ├── BaseGroup.class │ │ ├── LineGraph.class │ │ ├── QualityBoxPlot.class │ │ └── TileGraph.class │ │ ├── Help │ │ ├── HelpDialog.class │ │ ├── HelpIndexRoot$FileSorter.class │ │ ├── HelpIndexRoot.class │ │ ├── HelpPage.class │ │ ├── HelpPageDisplay$HelpEditor.class │ │ ├── HelpPageDisplay.class │ │ └── HelpSearchPanel.class │ │ ├── Modules │ │ ├── AbstractQCModule.class │ │ ├── AdapterContent$Adapter.class │ │ ├── AdapterContent$ResultsTable.class │ │ ├── AdapterContent.class │ │ ├── BasicStats$ResultsTable.class │ │ ├── BasicStats.class │ │ ├── DuplicationLevel.class │ │ ├── GCModel │ │ │ ├── GCModel.class │ │ │ └── GCModelValue.class │ │ ├── KmerContent$Kmer.class │ │ ├── KmerContent$ResultsTable.class │ │ ├── KmerContent.class │ │ ├── ModuleConfig.class │ │ ├── ModuleFactory.class │ │ ├── NContent.class │ │ ├── OverRepresentedSeqs$OverrepresentedSeq.class │ │ ├── OverRepresentedSeqs$ResultsTable.class │ │ ├── OverRepresentedSeqs.class │ │ ├── PerBaseQualityScores.class │ │ ├── PerBaseSequenceContent.class │ │ ├── PerSequenceGCContent.class │ │ ├── PerSequenceQualityScores.class │ │ ├── PerTileQualityScores.class │ │ ├── QCModule.class │ │ └── SequenceLengthDistribution.class │ │ ├── Report │ │ ├── HTMLReportArchive.class │ │ └── stylesheet.txt │ │ ├── Resources │ │ ├── error.png │ │ ├── fastqc_icon.png │ │ ├── fastqc_icon.svg │ │ ├── fastqc_icon_100.png │ │ ├── tick.png │ │ └── warning.png │ │ ├── Results │ │ ├── ResultsPanel$ModuleRenderer.class │ │ └── ResultsPanel.class │ │ ├── Sequence │ │ ├── BAMFile.class │ │ ├── Contaminant │ │ │ ├── Contaminant.class │ │ │ ├── ContaminantHit.class │ │ │ └── ContaminentFinder.class │ │ ├── Fast5File.class │ │ ├── FastQFile.class │ │ ├── QualityEncoding │ │ │ └── PhredEncoding.class │ │ ├── Sequence.class │ │ ├── SequenceFactory.class │ │ ├── SequenceFile.class │ │ ├── SequenceFileGroup.class │ │ └── SequenceFormatException.class │ │ ├── Statistics │ │ ├── NormalDistribution.class │ │ └── PearsonCorrelation.class │ │ └── Utilities │ │ ├── CasavaBasename.class │ │ ├── HotColdColourGradient.class │ │ ├── ImageToBase64.class │ │ ├── MultiMemberGZIPInputStream.class │ │ ├── NameFormatException.class │ │ ├── NanoporeBasename.class │ │ ├── QualityCount.class │ │ └── RGB.class │ ├── kallisto │ ├── README.md │ ├── kallisto │ ├── license.txt │ └── test │ │ ├── README.md │ │ ├── Snakefile │ │ ├── ind │ │ ├── kallisto_bin_Debug_0.42.4 │ │ ├── out │ │ ├── abundance.h5 │ │ ├── abundance.tsv │ │ └── run_info.json │ │ ├── reads_1.fastq.gz │ │ ├── reads_2.fastq.gz │ │ └── transcripts.fasta.gz │ ├── sratools │ └── bin │ │ ├── fastdump │ │ ├── fastdump.2 │ │ ├── fastdump.2.7.0 │ │ ├── fastq-dump │ │ ├── fastq-dump.2 │ │ └── fastq-dump.2.7.0 │ └── star │ └── STAR 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