CONTRIBUTING.rst
LICENSE
MANIFEST.in
README.rst
requirements.txt
requirements_dev.txt
requirements_pipelines.txt
requirements_rtd.txt
setup.cfg
setup.py
doc/minimalist.rules
doc/minimalist2.rules
doc/build/html/_downloads/ae97a5059078d67c3ea0d6270a372bea/minimalist2.rules
doc/build/html/_downloads/d4af52a810a0b922e7bab781bdcbcb1d/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/annotations.py
sequana/assembly.py
sequana/bamtools.py
sequana/bed.py
sequana/bedtools.py
sequana/busco.py
sequana/canu_scanner.py
sequana/chipseq.py
sequana/cigar.py
sequana/cnv.py
sequana/compare.py
sequana/contigs.py
sequana/coverage.py
sequana/cpg_islands.py
sequana/criteria.py
sequana/databases.py
sequana/datatools.py
sequana/demultiplex.py
sequana/enrichment.py
sequana/errors.py
sequana/expdesign.py
sequana/fasta.py
sequana/fastq.py
sequana/fastqc.py
sequana/featurecounts.py
sequana/find_motif.py
sequana/freebayes_bcf_filter.py
sequana/freebayes_vcf_filter.py
sequana/genbank.py
sequana/gff3.py
sequana/gtf.py
sequana/iem.py
sequana/iotools.py
sequana/isoseq.py
sequana/itol.py
sequana/iuapc.py
sequana/jsontool.py
sequana/kegg.py
sequana/kmer.py
sequana/kraken.py
sequana/kraken_builder.py
sequana/krona.py
sequana/laa.py
sequana/lazy.py
sequana/lazyimports.py
sequana/mgi.py
sequana/mh.py
sequana/misc.py
sequana/mixture.py
sequana/pacbio.py
sequana/pacbio_amplicon.py
sequana/phred.py
sequana/pipelines_common.py
sequana/protein.py
sequana/rnadiff.py
sequana/running_median.py
sequana/salmon.py
sequana/sequence.py
sequana/snaketools.py
sequana/sniffer.py
sequana/snpeff.py
sequana/stats.py
sequana/summary.py
sequana/taxonomy.py
sequana/tools.py
sequana/trf.py
sequana/vcf_filter.py
sequana/vcftools.py
sequana/vst.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/enrichment.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/rnadiff.py
sequana/modules_report/summary.py
sequana/modules_report/variant_calling.py
sequana/multiqc/__init__.py
sequana/multiqc/bamtools_stats.py
sequana/multiqc/config.py
sequana/multiqc/coverage.py
sequana/multiqc/isoseq.py
sequana/multiqc/isoseq_qc.py
sequana/multiqc/kraken.py
sequana/multiqc/laa.py
sequana/multiqc/multiqc_config.yaml
sequana/multiqc/pacbio_amplicon.py
sequana/multiqc/pacbio_qc.py
sequana/multiqc/quality_control.py
sequana/pipelines/__init__.py
sequana/pipelines/compressor/README.rst
sequana/pipelines/compressor/cluster_config.json
sequana/pipelines/compressor/compressor.rules
sequana/pipelines/compressor/config.yaml
sequana/pipelines/compressor/dag.png
sequana/pipelines/compressor/requirements.txt
sequana/pipelines/compressor/schema.yaml
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
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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/KO_ATCACG_R1_test.fastq.gz
sequana/resources/data/README.rst
sequana/resources/data/SIRV.fa
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sequana/resources/data/adapters/NEXTFlex48_DNA_revcomp.fa
sequana/resources/data/adapters/NEXTFlex96_DNA_fwd.fa
sequana/resources/data/adapters/NEXTFlex96_DNA_rev.fa
sequana/resources/data/adapters/NEXTFlex96_DNA_revcomp.fa
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sequana/resources/data/adapters/TruSeqCD_DNA_rev.fa
sequana/resources/data/adapters/TruSeqCD_DNA_revcomp.fa
sequana/resources/data/adapters/TruSeqCD_alt_DNA_fwd.fa
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sequana/resources/data/adapters/TruSeqCD_alt_DNA_revcomp.fa
sequana/resources/data/adapters/TruSeqUD_DNA_fwd.fa
sequana/resources/data/adapters/TruSeqUD_DNA_rev.fa
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sequana/resources/data/adapters/adapters_NEBNext_fwd.fa
sequana/resources/data/adapters/adapters_NEBNext_rev.fa
sequana/resources/data/adapters/adapters_NEBNext_revcomp.fa
sequana/resources/data/adapters/adapters_Nextera_fwd.fa
sequana/resources/data/adapters/adapters_Nextera_rev.fa
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sequana/resources/data/adapters/adapters_Small_fwd.fa
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sequana/resources/data/adapters/adapters_Small_revcomp.fa
sequana/resources/data/adapters/adapters_TruSeq_fwd.fa
sequana/resources/data/adapters/adapters_TruSeq_rev.fa
sequana/resources/data/adapters/adapters_TruSeq_revcomp.fa
sequana/resources/images/Institut_Pasteur.png
sequana/resources/images/__init__.py
sequana/resources/images/no_data.jpg
sequana/resources/images/no_data.png
sequana/resources/js/__init__.py
sequana/resources/js/bootstrap.min.js
sequana/resources/js/buttons.html5.min.js
sequana/resources/js/buttons.print.min.js
sequana/resources/js/canvasjs.min.js
sequana/resources/js/dataTables.buttons.min.js
sequana/resources/js/jquery-2.1.1.js
sequana/resources/js/jquery-3.1.1.min.js
sequana/resources/js/jquery-3.2.1.min.js
sequana/resources/js/jquery-3.5.1.min.js
sequana/resources/js/jquery.dataTables.min.js
sequana/resources/js/jquery.dropdown.min.js
sequana/resources/js/jquery.tocPlugin.js
sequana/resources/js/papaparse.min.js
sequana/resources/snpeff/__init__.py
sequana/resources/snpeff/snpEff.config
sequana/resources/templates/__init__.py
sequana/resources/templates/base.html
sequana/resources/templates/joint_calling.html
sequana/resources/templates/rnadiff_light_template.R
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sequana/resources/testing/README.rst
sequana/resources/testing/__init__.py
sequana/resources/testing/adapters_with_duplicates.fa
sequana/resources/testing/measles.fa
sequana/resources/testing/measles.fa.fai
sequana/resources/testing/saccer3_truncated.gff
sequana/resources/testing/summary_bamtools_stats.txt
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sequana/resources/testing/summary_kraken.json
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sequana/resources/testing/test_expdesign_generic.csv
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sequana/rules/README.rst
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sequana/rules/Adapters/__init__.py
sequana/rules/Adapters/adapter_removal/adapter_removal.rules
sequana/rules/Adapters/alien_trimmer/alien_trimmer.rules
sequana/rules/Adapters/cutadapt/cutadapt.rules
sequana/rules/Adapters/identify_adapters/identify_adapters.rules
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sequana/rules/Assembly/busco/busco.rules
sequana/rules/Assembly/busco_analysis/busco_analysis.rules
sequana/rules/Assembly/canu/canu.rules
sequana/rules/Assembly/spades/spades.rules
sequana/rules/Assembly/spades_get_fastq/spades_get_fastq.rules
sequana/rules/DupRadar/DupRadar.rules
sequana/rules/Pacbio/__init__.py
sequana/rules/SARTools/SARTools.rules
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sequana/rules/SnpEff/snpeff/1.1/snpeff.rules
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sequana/rules/Utils/dynamic_unpigz/dynamic_unpigz.rules
sequana/rules/Utils/dynamic_vcf_to_bcf/dynamic_vcf_to_bcf.rules
sequana/rules/Variant_caller/__init__.py
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sequana/rules/Variant_caller/freebayes_bcf_filter/freebayes_bcf_filter.rules
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sequana/rules/idr/preIDR_dynamic/preIDR_dynamic.rules
sequana/rules/idr/select_peaks/select_peaks.rules
sequana/rules/idr/stats_peakCalling/stats_peakCalling.rules
sequana/rules/idr/union_peaks/union_peaks.rules
sequana/rules/igvtools/igvtools.rules
sequana/rules/indel_realigner/indel_realigner.rules
sequana/rules/kraken/1.0/kraken.rules
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sequana/rules/macs3_dynamic/macs3_dynamic.rules
sequana/rules/mapping_analysis/mapping_analysis.rules
sequana/rules/miRNA_count_dynamic/miRNA_count_dynamic.rules
sequana/rules/multiqc/multiqc.rules
sequana/rules/multiqc/2.0/multiqc.rules
sequana/rules/multiqc2/multiqc2.rules
sequana/rules/pacbio_quality/pacbio_quality.rules
sequana/rules/peak_calling/macs2_dynamic/macs2_dynamic.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_dynamic/mark_duplicates_dynamic.rules
sequana/rules/picard-tools/reorderSam/reorderSam.rules
sequana/rules/preSARTools/preSARTools.rules
sequana/rules/prokka/prokka.rules
sequana/rules/quast/quast.rules
sequana/rules/remove_blacklist/remove_blacklist.rules
sequana/rules/revcomp_rule/revcomp_rule.rules
sequana/rules/rnaseqc/rnaseqc.rules
sequana/rules/rulegraph/rulegraph.rules
sequana/rules/salmon_index/salmon_index.rules
sequana/rules/salmon_mapping/salmon_mapping.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/spikes_counting/spikes_counting.rules
sequana/rules/spp/spp.rules
sequana/rules/star_index/star_index.rules
sequana/rules/star_mapping/star_mapping.rules
sequana/rules/summary_pipeline/summary_pipeline.rules
sequana/rules/tophat_mapping/tophat_mapping.rules
sequana/scripts/__init__.py
sequana/scripts/bam_splitter.py
sequana/scripts/browser.py
sequana/scripts/compressor.py
sequana/scripts/coverage.py
sequana/scripts/fixR1R2.py
sequana/scripts/lane_merging.py
sequana/scripts/main.py
sequana/scripts/mapping.py
sequana/scripts/start_pipeline.py
sequana/scripts/substractor.py
sequana/scripts/taxonomy.py
sequana/scripts/tools.py
sequana/scripts/vcf_filter.py
sequana/sphinxext/__init__.py
sequana/sphinxext/sequana_pipeline.py
sequana/sphinxext/snakemakerule.py
sequana/utils/__init__.py
sequana/utils/config.py
sequana/utils/datatables_js.py
sequana/utils/tree.py
sequana/viz/__init__.py
sequana/viz/anova.py
sequana/viz/boxplot.py
sequana/viz/clusterisation.py
sequana/viz/core.py
sequana/viz/corrplot.py
sequana/viz/dendogram.py
sequana/viz/heatmap.py
sequana/viz/hinton.py
sequana/viz/hist2d.py
sequana/viz/imshow.py
sequana/viz/isomap.py
sequana/viz/linkage.py
sequana/viz/mds.py
sequana/viz/pca.py
sequana/viz/scatter.py
sequana/viz/venn.py
sequana/viz/volcano.py