CONTRIBUTING.rst
LICENSE
MANIFEST.in
README.rst
requirements.txt
requirements_dev.txt
requirements_pipelines.txt
setup.cfg
setup.py
analysis/quality_control.rules
doc/minimalist.rules
doc/minimalist2.rules
doc/toy.rules
doc/build/html/_downloads/minimalist.rules
doc/build/html/_downloads/minimalist2.rules
doc/test/minimalist.rules
examples/README.txt
examples/plot_bam.py
examples/plot_coverage.py
examples/plot_fastqc_hist.py
examples/plot_kraken.py
examples/plot_pipeline_stats.py
examples/plot_qc_pacbio.py
examples/plot_running_median.py
sequana/__init__.py
sequana/adapters.py
sequana/assembly.py
sequana/bamtools.py
sequana/bedtools.py
sequana/busco.py
sequana/coverage.py
sequana/databases.py
sequana/datatools.py
sequana/errors.py
sequana/expdesign.py
sequana/fasta.py
sequana/fastq.py
sequana/freebayes_bcf_filter.py
sequana/freebayes_vcf_filter.py
sequana/iotools.py
sequana/jsontool.py
sequana/kmer.py
sequana/kraken.py
sequana/kraken_builder.py
sequana/krona.py
sequana/lazy.py
sequana/lazyimports.py
sequana/misc.py
sequana/pacbio.py
sequana/phred.py
sequana/running_median.py
sequana/sequence.py
sequana/simulation.py
sequana/snaketools.py
sequana/snpeff.py
sequana/stats.py
sequana/tools.py
sequana.egg-info/PKG-INFO
sequana.egg-info/SOURCES.txt
sequana.egg-info/dependency_links.txt
sequana.egg-info/entry_points.txt
sequana.egg-info/not-zip-safe
sequana.egg-info/requires.txt
sequana.egg-info/top_level.txt
sequana/gui/__init__.py
sequana/gui/about.py
sequana/gui/browser.py
sequana/gui/file_browser.py
sequana/gui/help.py
sequana/gui/ipython.py
sequana/gui/messages.py
sequana/gui/preferences.py
sequana/gui/sequana_gui.py
sequana/gui/snakemake.py
sequana/gui/tools.py
sequana/gui/ui_help.py
sequana/gui/ui_mainwindow.py
sequana/gui/ui_preferences.py
sequana/gui/ui_snakemake.py
sequana/gui/widgets.py
sequana/modules_report/__init__.py
sequana/modules_report/bamqc.py
sequana/modules_report/base_module.py
sequana/modules_report/bwa_bam_to_fastq.py
sequana/modules_report/coverage.py
sequana/modules_report/cutadapt.py
sequana/modules_report/fastq_stats.py
sequana/modules_report/fastqc.py
sequana/modules_report/joint_calling.py
sequana/modules_report/kraken.py
sequana/modules_report/multi_summary.py
sequana/modules_report/pacbio_input_bam.py
sequana/modules_report/phix.py
sequana/modules_report/quast.py
sequana/modules_report/summary.py
sequana/modules_report/variant_calling.py
sequana/multiqc/__init__.py
sequana/multiqc/pacbio_qc.py
sequana/multiqc/quality_control.py
sequana/pipelines/__init__.py
sequana/pipelines/config.yaml
sequana/pipelines/atac-seq/atac-seq.rules
sequana/pipelines/atac-seq/config.yaml
sequana/pipelines/compressor/compressor.rules
sequana/pipelines/compressor/config.yaml
sequana/pipelines/denovo_assembly/config.yaml
sequana/pipelines/denovo_assembly/denovo_assembly.rules
sequana/pipelines/pacbio_denovo/config.yaml
sequana/pipelines/pacbio_denovo/pacbio_denovo.rules
sequana/pipelines/pacbio_qc/config.yaml
sequana/pipelines/pacbio_qc/pacbio_qc.rules
sequana/pipelines/quality_control/config.yaml
sequana/pipelines/quality_control/quality_control.rules
sequana/pipelines/rnaseq/config.yaml
sequana/pipelines/rnaseq/multiqc_config.yaml
sequana/pipelines/rnaseq/rnaseq.rules
sequana/pipelines/smallrnaseq/config.yaml
sequana/pipelines/smallrnaseq/multiqc_config.yaml
sequana/pipelines/smallrnaseq/smallrnaseq.rules
sequana/pipelines/variant_calling/config.yaml
sequana/pipelines/variant_calling/variant_calling.rules
sequana/plots/__init__.py
sequana/plots/canvasjs_base.py
sequana/plots/canvasjs_linegraph.py
sequana/resources/__init__.py
sequana/resources/busco/__init__.py
sequana/resources/busco/config.ini
sequana/resources/canvas/__init__.py
sequana/resources/canvas/bar.py
sequana/resources/css/__init__.py
sequana/resources/css/bootstrap.min.css
sequana/resources/css/buttons.dataTables.min.css
sequana/resources/css/jquery.dataTables.min.css
sequana/resources/css/jquery.dropdown.min.css
sequana/resources/css/report.css
sequana/resources/data/Hm2_GTGAAA_L005_R1_001.fastq.gz
sequana/resources/data/Hm2_GTGAAA_L005_R2_001.fastq.gz
sequana/resources/data/JB409847.bcf
sequana/resources/data/JB409847.bed
sequana/resources/data/JB409847.cov.csv
sequana/resources/data/JB409847.csv
sequana/resources/data/JB409847.expected.vcf
sequana/resources/data/JB409847.fasta
sequana/resources/data/JB409847.filter.vcf
sequana/resources/data/JB409847.gbk
sequana/resources/data/JB409847.vc.csv
sequana/resources/data/JB409847.vcf
sequana/resources/data/KO_ATCACG_L001_R1_001.fastq.gz
sequana/resources/data/README.rst
sequana/resources/data/WT_ATCACG_L001_R1_001.fastq.gz
sequana/resources/data/__init__.py
sequana/resources/data/measles.fa
sequana/resources/data/measles.fa.amb
sequana/resources/data/measles.fa.ann
sequana/resources/data/measles.fa.bam
sequana/resources/data/measles.fa.bwt
sequana/resources/data/measles.fa.pac
sequana/resources/data/measles.fa.sa
sequana/resources/data/measles.fa.sorted.bam
sequana/resources/data/phiX174.fa
sequana/resources/data/virus.bed
sequana/resources/data/adapters/README.rst
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sequana/rules/mapping_analysis/mapping_analysis.rules
sequana/rules/miRNA_count_dynamic/miRNA_count_dynamic.rules
sequana/rules/multiqc/multiqc.rules
sequana/rules/peak_calling/macs2/macs2.rules
sequana/rules/picard-tools/__init__.py
sequana/rules/picard-tools/CollectInsertSizeMetrics/CollectInsertSizeMetrics.rules
sequana/rules/picard-tools/add_read_group/add_read_group.rules
sequana/rules/picard-tools/create_sequence_dictionary/create_sequence_dictionary.rules
sequana/rules/picard-tools/mark_duplicates/mark_duplicates.rules
sequana/rules/picard-tools/reorderSam/reorderSam.rules
sequana/rules/prokka/prokka.rules
sequana/rules/quast/quast.rules
sequana/rules/sambamba/__init__.py
sequana/rules/sambamba/sambamba_filter/sambamba_filter.rules
sequana/rules/sambamba/sambamba_markdup/sambamba_markdup.rules
sequana/rules/samtools_depth/samtools_depth.rules
sequana/rules/samtools_sort/samtools_sort.rules
sequana/rules/sequana_coverage/sequana_coverage.rules
sequana/rules/summary_pipeline/summary_pipeline.rules
sequana/rules/syntview/syntview.rules
sequana/scripts/__init__.py
sequana/scripts/browser.py
sequana/scripts/compressor.py
sequana/scripts/coverage.py
sequana/scripts/fastq_count.py
sequana/scripts/fastq_head.py
sequana/scripts/main.py
sequana/scripts/mapping.py
sequana/scripts/reports.py
sequana/scripts/summary.py
sequana/scripts/taxonomy.py
sequana/scripts/tools.py
sequana/sphinxext/__init__.py
sequana/sphinxext/snakemakerule.py
sequana/utils/__init__.py
sequana/utils/config.py
sequana/utils/datatables_js.py