LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
multiqc/__init__.py
multiqc/__main__.py
multiqc/multiqc.py
multiqc.egg-info/PKG-INFO
multiqc.egg-info/SOURCES.txt
multiqc.egg-info/dependency_links.txt
multiqc.egg-info/entry_points.txt
multiqc.egg-info/not-zip-safe
multiqc.egg-info/requires.txt
multiqc.egg-info/top_level.txt
multiqc/modules/__init__.py
multiqc/modules/base_module.py
multiqc/modules/adapterRemoval/__init__.py
multiqc/modules/adapterRemoval/adapterRemoval.py
multiqc/modules/afterqc/__init__.py
multiqc/modules/afterqc/afterqc.py
multiqc/modules/anglerfish/__init__.py
multiqc/modules/anglerfish/anglerfish.py
multiqc/modules/bamtools/__init__.py
multiqc/modules/bamtools/bamtools.py
multiqc/modules/bamtools/stats.py
multiqc/modules/bbduk/__init__.py
multiqc/modules/bbduk/bbduk.py
multiqc/modules/bbmap/__init__.py
multiqc/modules/bbmap/bbmap.py
multiqc/modules/bbmap/bbmap_filetypes.py
multiqc/modules/bbmap/plot_aqhist.py
multiqc/modules/bbmap/plot_basic_hist.py
multiqc/modules/bbmap/plot_bhist.py
multiqc/modules/bbmap/plot_bqhist.py
multiqc/modules/bbmap/plot_covhist.py
multiqc/modules/bbmap/plot_idhist.py
multiqc/modules/bbmap/plot_ihist.py
multiqc/modules/bbmap/plot_indelhist.py
multiqc/modules/bbmap/plot_mhist.py
multiqc/modules/bbmap/plot_qahist.py
multiqc/modules/bbmap/plot_qchist.py
multiqc/modules/bbmap/plot_qhist.py
multiqc/modules/bcftools/__init__.py
multiqc/modules/bcftools/bcftools.py
multiqc/modules/bcftools/stats.py
multiqc/modules/bcl2fastq/__init__.py
multiqc/modules/bcl2fastq/bcl2fastq.py
multiqc/modules/bclconvert/__init__.py
multiqc/modules/bclconvert/bclconvert.py
multiqc/modules/biobambam2/__init__.py
multiqc/modules/biobambam2/biobambam2.py
multiqc/modules/biobloomtools/__init__.py
multiqc/modules/biobloomtools/biobloomtools.py
multiqc/modules/biscuit/__init__.py
multiqc/modules/biscuit/biscuit.py
multiqc/modules/bismark/__init__.py
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multiqc/modules/bowtie1/__init__.py
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multiqc/modules/bustools/__init__.py
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multiqc/modules/ccs/__init__.py
multiqc/modules/ccs/ccs.py
multiqc/modules/cellranger/__init__.py
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multiqc/modules/cellranger/cellranger.py
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multiqc/modules/cellranger/vdj.py
multiqc/modules/checkqc/__init__.py
multiqc/modules/checkqc/checkqc.py
multiqc/modules/clipandmerge/__init__.py
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multiqc/modules/clusterflow/__init__.py
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multiqc/modules/conpair/__init__.py
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multiqc/modules/cutadapt/__init__.py
multiqc/modules/cutadapt/cutadapt.py
multiqc/modules/damageprofiler/__init__.py
multiqc/modules/damageprofiler/damageprofiler.py
multiqc/modules/dedup/__init__.py
multiqc/modules/dedup/dedup.py
multiqc/modules/deeptools/__init__.py
multiqc/modules/deeptools/bamPEFragmentSizeDistribution.py
multiqc/modules/deeptools/bamPEFragmentSizeTable.py
multiqc/modules/deeptools/deeptools.py
multiqc/modules/deeptools/estimateReadFiltering.py
multiqc/modules/deeptools/plotCorrelation.py
multiqc/modules/deeptools/plotCoverage.py
multiqc/modules/deeptools/plotEnrichment.py
multiqc/modules/deeptools/plotFingerprint.py
multiqc/modules/deeptools/plotPCA.py
multiqc/modules/deeptools/plotProfile.py
multiqc/modules/diamond/__init__.py
multiqc/modules/diamond/diamond.py
multiqc/modules/disambiguate/__init__.py
multiqc/modules/disambiguate/disambiguate.py
multiqc/modules/dragen/__init__.py
multiqc/modules/dragen/coverage_hist.py
multiqc/modules/dragen/coverage_metrics.py
multiqc/modules/dragen/coverage_per_contig.py
multiqc/modules/dragen/dragen.py
multiqc/modules/dragen/dragen_gc_metrics.py
multiqc/modules/dragen/fragment_length.py
multiqc/modules/dragen/mapping_metrics.py
multiqc/modules/dragen/ploidy_estimation_metrics.py
multiqc/modules/dragen/rna_quant_metrics.py
multiqc/modules/dragen/rna_transcript_cov.py
multiqc/modules/dragen/sc_atac_metrics.py
multiqc/modules/dragen/sc_rna_metrics.py
multiqc/modules/dragen/time_metrics.py
multiqc/modules/dragen/trimmer_metrics.py
multiqc/modules/dragen/utils.py
multiqc/modules/dragen/vc_metrics.py
multiqc/modules/dragen_fastqc/__init__.py
multiqc/modules/dragen_fastqc/base_metrics.py
multiqc/modules/dragen_fastqc/content_metrics.py
multiqc/modules/dragen_fastqc/dragen_fastqc.py
multiqc/modules/dragen_fastqc/gc_metrics.py
multiqc/modules/dragen_fastqc/read_metrics.py
multiqc/modules/dragen_fastqc/util.py
multiqc/modules/dragen_fastqc/assets/js/multiqc_dragen_fastqc.js
multiqc/modules/eigenstratdatabasetools/__init__.py
multiqc/modules/eigenstratdatabasetools/eigenstratdatabasetools.py
multiqc/modules/fastp/__init__.py
multiqc/modules/fastp/fastp.py
multiqc/modules/fastq_screen/__init__.py
multiqc/modules/fastq_screen/fastq_screen.py
multiqc/modules/fastqc/__init__.py
multiqc/modules/fastqc/fastqc.py
multiqc/modules/fastqc/assets/css/multiqc_fastqc.css
multiqc/modules/fastqc/assets/js/multiqc_fastqc.js
multiqc/modules/fastqc/fastqc_theoretical_gc/fastqc_theoretical_gc_hg38_genome.txt
multiqc/modules/fastqc/fastqc_theoretical_gc/fastqc_theoretical_gc_hg38_txome.txt
multiqc/modules/fastqc/fastqc_theoretical_gc/fastqc_theoretical_gc_mm10_genome.txt
multiqc/modules/fastqc/fastqc_theoretical_gc/fastqc_theoretical_gc_mm10_txome.txt
multiqc/modules/featureCounts/__init__.py
multiqc/modules/featureCounts/feature_counts.py
multiqc/modules/fgbio/ErrorRateByReadPosition.py
multiqc/modules/fgbio/__init__.py
multiqc/modules/fgbio/fgbio.py
multiqc/modules/fgbio/groupreadsbyumi.py
multiqc/modules/filtlong/__init__.py
multiqc/modules/filtlong/filtlong.py
multiqc/modules/flash/__init__.py
multiqc/modules/flash/flash.py
multiqc/modules/flexbar/__init__.py
multiqc/modules/flexbar/flexbar.py
multiqc/modules/gatk/__init__.py
multiqc/modules/gatk/base_recalibrator.py
multiqc/modules/gatk/gatk.py
multiqc/modules/gatk/varianteval.py
multiqc/modules/gffcompare/__init__.py
multiqc/modules/gffcompare/gffcompare.py
multiqc/modules/goleft_indexcov/__init__.py
multiqc/modules/goleft_indexcov/goleft_indexcov.py
multiqc/modules/gopeaks/__init__.py
multiqc/modules/gopeaks/gopeaks.py
multiqc/modules/happy/__init__.py
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multiqc/modules/hicexplorer/__init__.py
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multiqc/modules/hicpro/__init__.py
multiqc/modules/hicpro/hicpro.py
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multiqc/modules/hifiasm/__init__.py
multiqc/modules/hifiasm/hifiasm.py
multiqc/modules/hisat2/__init__.py
multiqc/modules/hisat2/hisat2.py
multiqc/modules/homer/__init__.py
multiqc/modules/homer/findpeaks.py
multiqc/modules/homer/homer.py
multiqc/modules/homer/tagdirectory.py
multiqc/modules/hops/__init__.py
multiqc/modules/hops/hops.py
multiqc/modules/htseq/__init__.py
multiqc/modules/htseq/htseq.py
multiqc/modules/humid/__init__.py
multiqc/modules/humid/humid.py
multiqc/modules/interop/__init__.py
multiqc/modules/interop/interop.py
multiqc/modules/ivar/__init__.py
multiqc/modules/ivar/ivar.py
multiqc/modules/jcvi/__init__.py
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multiqc/modules/jellyfish/__init__.py
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multiqc/modules/kaiju/__init__.py
multiqc/modules/kaiju/kaiju.py
multiqc/modules/kallisto/__init__.py
multiqc/modules/kallisto/kallisto.py
multiqc/modules/kat/__init__.py
multiqc/modules/kat/kat.py
multiqc/modules/kraken/__init__.py
multiqc/modules/kraken/kraken.py
multiqc/modules/leehom/__init__.py
multiqc/modules/leehom/leehom.py
multiqc/modules/lima/__init__.py
multiqc/modules/lima/lima.py
multiqc/modules/longranger/__init__.py
multiqc/modules/longranger/longranger.py
multiqc/modules/macs2/__init__.py
multiqc/modules/macs2/macs2.py
multiqc/modules/malt/__init__.py
multiqc/modules/malt/malt.py
multiqc/modules/methylQA/__init__.py
multiqc/modules/methylQA/methylQA.py
multiqc/modules/minionqc/__init__.py
multiqc/modules/minionqc/minionqc.py
multiqc/modules/mirtop/__init__.py
multiqc/modules/mirtop/mirtop.py
multiqc/modules/mirtrace/__init__.py
multiqc/modules/mirtrace/mirtrace.py
multiqc/modules/mosdepth/__init__.py
multiqc/modules/mosdepth/mosdepth.py
multiqc/modules/motus/__init__.py
multiqc/modules/motus/motus.py
multiqc/modules/mtnucratio/__init__.py
multiqc/modules/mtnucratio/mtnucratio.py
multiqc/modules/multivcfanalyzer/__init__.py
multiqc/modules/multivcfanalyzer/multivcfanalyzer.py
multiqc/modules/nanostat/__init__.py
multiqc/modules/nanostat/nanostat.py
multiqc/modules/nextclade/__init__.py
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multiqc/modules/ngsderive/__init__.py
multiqc/modules/ngsderive/ngsderive.py
multiqc/modules/odgi/__init__.py
multiqc/modules/odgi/odgi.py
multiqc/modules/optitype/__init__.py
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multiqc/modules/pangolin/__init__.py
multiqc/modules/pangolin/pangolin.py
multiqc/modules/pbmarkdup/__init__.py
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multiqc/modules/peddy/__init__.py
multiqc/modules/peddy/peddy.py
multiqc/modules/phantompeakqualtools/__init__.py
multiqc/modules/phantompeakqualtools/phantompeakqualtools.py
multiqc/modules/picard/AlignmentSummaryMetrics.py
multiqc/modules/picard/BaseDistributionByCycleMetrics.py
multiqc/modules/picard/CollectIlluminaBasecallingMetrics.py
multiqc/modules/picard/CollectIlluminaLaneMetrics.py
multiqc/modules/picard/CrosscheckFingerprints.py
multiqc/modules/picard/ExtractIlluminaBarcodes.py
multiqc/modules/picard/GcBiasMetrics.py
multiqc/modules/picard/HsMetrics.py
multiqc/modules/picard/InsertSizeMetrics.py
multiqc/modules/picard/MarkDuplicates.py
multiqc/modules/picard/MarkIlluminaAdapters.py
multiqc/modules/picard/OxoGMetrics.py
multiqc/modules/picard/QualityByCycleMetrics.py
multiqc/modules/picard/QualityScoreDistributionMetrics.py
multiqc/modules/picard/QualityYieldMetrics.py
multiqc/modules/picard/RnaSeqMetrics.py
multiqc/modules/picard/RrbsSummaryMetrics.py
multiqc/modules/picard/TargetedPcrMetrics.py
multiqc/modules/picard/ValidateSamFile.py
multiqc/modules/picard/VariantCallingMetrics.py
multiqc/modules/picard/WgsMetrics.py
multiqc/modules/picard/__init__.py
multiqc/modules/picard/picard.py
multiqc/modules/picard/util.py
multiqc/modules/porechop/__init__.py
multiqc/modules/porechop/porechop.py
multiqc/modules/preseq/__init__.py
multiqc/modules/preseq/preseq.py
multiqc/modules/prinseqplusplus/__init__.py
multiqc/modules/prinseqplusplus/prinseqplusplus.py
multiqc/modules/prokka/__init__.py
multiqc/modules/prokka/prokka.py
multiqc/modules/purple/__init__.py
multiqc/modules/purple/purple.py
multiqc/modules/pychopper/__init__.py
multiqc/modules/pychopper/pychopper.py
multiqc/modules/pycoqc/__init__.py
multiqc/modules/pycoqc/pycoqc.py
multiqc/modules/qc3C/__init__.py
multiqc/modules/qc3C/qc3C.py
multiqc/modules/qorts/__init__.py
multiqc/modules/qorts/qorts.py
multiqc/modules/qualimap/QM_BamQC.py
multiqc/modules/qualimap/QM_RNASeq.py
multiqc/modules/qualimap/__init__.py
multiqc/modules/qualimap/qualimap.py
multiqc/modules/quast/__init__.py
multiqc/modules/quast/quast.py
multiqc/modules/rna_seqc/__init__.py
multiqc/modules/rna_seqc/rna_seqc.py
multiqc/modules/rockhopper/__init__.py
multiqc/modules/rockhopper/rockhopper.py
multiqc/modules/rsem/__init__.py
multiqc/modules/rsem/rsem.py
multiqc/modules/rseqc/__init__.py
multiqc/modules/rseqc/bam_stat.py
multiqc/modules/rseqc/gene_body_coverage.py
multiqc/modules/rseqc/infer_experiment.py
multiqc/modules/rseqc/inner_distance.py
multiqc/modules/rseqc/junction_annotation.py
multiqc/modules/rseqc/junction_saturation.py
multiqc/modules/rseqc/read_distribution.py
multiqc/modules/rseqc/read_duplication.py
multiqc/modules/rseqc/read_gc.py
multiqc/modules/rseqc/rseqc.py
multiqc/modules/rseqc/tin.py
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multiqc/modules/salmon/__init__.py
multiqc/modules/salmon/salmon.py
multiqc/modules/sambamba/__init__.py
multiqc/modules/sambamba/markdup.py
multiqc/modules/sambamba/sambamba.py
multiqc/modules/samblaster/__init__.py
multiqc/modules/samblaster/samblaster.py
multiqc/modules/samtools/__init__.py
multiqc/modules/samtools/flagstat.py
multiqc/modules/samtools/idxstats.py
multiqc/modules/samtools/rmdup.py
multiqc/modules/samtools/samtools.py
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multiqc/modules/sargasso/__init__.py
multiqc/modules/sargasso/sargasso.py
multiqc/modules/sentieon/AlignmentSummaryMetrics.py
multiqc/modules/sentieon/GcBiasMetrics.py
multiqc/modules/sentieon/InsertSizeMetrics.py
multiqc/modules/sentieon/__init__.py
multiqc/modules/sentieon/sentieon.py
multiqc/modules/seqyclean/__init__.py
multiqc/modules/seqyclean/seqyclean.py
multiqc/modules/sexdeterrmine/__init__.py
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multiqc/modules/slamdunk/__init__.py
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multiqc/modules/snpsplit/__init__.py
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multiqc/modules/supernova/__init__.py
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multiqc/modules/umitools/__init__.py
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multiqc/modules/verifybamid/__init__.py
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