CONTRIBUTING.rst
LICENSE
MANIFEST.in
README.rst
requirements.txt
requirements_dev.txt
requirements_pipelines.txt
requirements_pipelines_extra.txt
setup.cfg
setup.py
doc/minimalist.rules
doc/minimalist2.rules
doc/toy.rules
doc/build/html/_downloads/minimalist.rules
doc/build/html/_downloads/minimalist2.rules
doc/build/json/_downloads/minimalist.rules
doc/build/json/_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/canu_scanner.py
sequana/cigar.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/isoseq.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/vcf_filter.py
sequana/vcftools.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/KO_ATCACG_R1_test.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.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
sequana/resources/data/adapters/__init__.py
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
sequana/resources/data/adapters/adapters_Nextera_revcomp.fa
sequana/resources/data/adapters/adapters_PCRFree_fwd.fa
sequana/resources/data/adapters/adapters_PCRFree_rev.fa
sequana/resources/data/adapters/adapters_PCRFree_revcomp.fa
sequana/resources/data/adapters/adapters_Rubicon_fwd.fa
sequana/resources/data/adapters/adapters_Rubicon_rev.fa
sequana/resources/data/adapters/adapters_Rubicon_revcomp.fa
sequana/resources/data/adapters/adapters_SMARTer_fwd.fa
sequana/resources/data/adapters/adapters_SMARTer_rev.fa
sequana/resources/data/adapters/adapters_SMARTer_revcomp.fa
sequana/resources/data/adapters/adapters_Small_fwd.fa
sequana/resources/data/adapters/adapters_Small_rev.fa
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/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.dataTables.min.js
sequana/resources/js/jquery.dropdown.min.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/standard.html
sequana/resources/testing/README.rst
sequana/resources/testing/__init__.py
sequana/resources/testing/adapters_with_duplicates.fa
sequana/resources/testing/filtered.vcf
sequana/resources/testing/remaining.vcf
sequana/resources/testing/summary_pacbio_qc1.json
sequana/resources/testing/summary_pacbio_qc2.json
sequana/resources/testing/summary_pacbio_qc3.json
sequana/resources/testing/summary_qc.json
sequana/resources/testing/test.bam
sequana/resources/testing/test.fasta
sequana/resources/testing/test.fastq
sequana/resources/testing/test.fastq.gz
sequana/resources/testing/test.sam
sequana/resources/testing/test.vcf
sequana/resources/testing/test_1_1000.fastq.gz
sequana/resources/testing/test_JB409847.bed
sequana/resources/testing/test_R1_.mapped.fastq
sequana/resources/testing/test_R1_.unmapped.fastq
sequana/resources/testing/test_R2_.mapped.fastq
sequana/resources/testing/test_R2_.unmapped.fastq
sequana/resources/testing/test_adapter_removal_output.txt
sequana/resources/testing/test_atropos_paired.txt
sequana/resources/testing/test_atropos_pe.json
sequana/resources/testing/test_atropos_pe.txt
sequana/resources/testing/test_atropos_se.json
sequana/resources/testing/test_atropos_se.txt
sequana/resources/testing/test_blast_ebi.xml
sequana/resources/testing/test_blast_local.xml
sequana/resources/testing/test_busco_full_table.tsv
sequana/resources/testing/test_coverage.csv
sequana/resources/testing/test_cutadapt_paired.txt
sequana/resources/testing/test_dag.ann.dot
sequana/resources/testing/test_dag.dot
sequana/resources/testing/test_expdesign_generic.csv
sequana/resources/testing/test_expdesign_hiseq.csv
sequana/resources/testing/test_expdesign_hiseq_doubleindex.csv
sequana/resources/testing/test_expdesign_hiseq_duplicated_index.csv
sequana/resources/testing/test_expdesign_miseq_illumina.csv
sequana/resources/testing/test_expdesign_miseq_illumina2.csv
sequana/resources/testing/test_expdesign_miseq_illumina_1.csv
sequana/resources/testing/test_expdesign_rubicon.csv
sequana/resources/testing/test_expdesign_wrong.csv
sequana/resources/testing/test_fasta.fasta
sequana/resources/testing/test_gui_generic_config.yaml
sequana/resources/testing/test_gui_generic_snakefile_config.rules
sequana/resources/testing/test_gui_generic_snakefile_configfile.rules
sequana/resources/testing/test_gui_generic_snakefile_noconfig.rules
sequana/resources/testing/test_index_mapper.csv
sequana/resources/testing/test_kraken.out
sequana/resources/testing/test_kraken.out.summary
sequana/resources/testing/test_krona_k1.tsv
sequana/resources/testing/test_krona_k2.tsv
sequana/resources/testing/test_pacbio_subreads.bam
sequana/resources/testing/test_snakemake_stats.txt
sequana/resources/testing/test_snpeff_ref.gb
sequana/resources/testing/test_summary_fastq_stats.json
sequana/resources/testing/test_summary_module.svg
sequana/resources/testing/test_taxon_rtd.csv
sequana/resources/testing/test_vcf_mpileup_4dot1.vcf
sequana/rules/README.rst
sequana/rules/__init__.py
sequana/rules/Adapters/__init__.py
sequana/rules/Adapters/adapter_removal/adapter_removal.rules
sequana/rules/Adapters/alien_trimmer/alien_trimmer.rules
sequana/rules/Adapters/clean_ngs/clean_ngs.rules
sequana/rules/Adapters/cutadapt/cutadapt.rules
sequana/rules/Adapters/identify_adapters/identify_adapters.rules
sequana/rules/Adapters/skewer/skewer.rules
sequana/rules/Assembly/__init__.py
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/Dev/kraken_adapters/kraken_adapters.rules
sequana/rules/DupRadar/DupRadar.rules
sequana/rules/Mapping/__init__.py
sequana/rules/Mapping/bowtie1_index_dynamic/bowtie1_index_dynamic.rules
sequana/rules/Mapping/bowtie1_mapping_dynamic/bowtie1_mapping_dynamic.rules
sequana/rules/Mapping/bowtie2_index/bowtie2_index.rules
sequana/rules/Mapping/bowtie2_mapping/bowtie2_mapping.rules
sequana/rules/Mapping/star_index/star_index.rules
sequana/rules/Mapping/star_mapping/star_mapping.rules
sequana/rules/Mapping/tophat_mapping/tophat_mapping.rules
sequana/rules/Misc/conda/conda.rules
sequana/rules/Misc/dag/dag.rules
sequana/rules/Misc/extract_fasta_from_bed/extract_fasta_from_bed.rules
sequana/rules/Misc/rulegraph/rulegraph.rules
sequana/rules/Pacbio/__init__.py
sequana/rules/Pacbio/pacbio_quality/pacbio_quality.rules
sequana/rules/RNAseQC/RNAseQC.rules
sequana/rules/SnpEff/__init__.py
sequana/rules/SnpEff/snpeff/snpeff.rules
sequana/rules/SnpEff/snpeff_add_locus_in_fasta/snpeff_add_locus_in_fasta.rules
sequana/rules/SnpEff/snpeff_create_database/snpeff_create_database.rules
sequana/rules/SnpEff/snpeff_dynamic/snpeff_dynamic.rules
sequana/rules/Taxonomy/__init__.py
sequana/rules/Taxonomy/fastq_screen/fastq_screen.rules
sequana/rules/Taxonomy/fastq_screen_report/fastq_screen_report.rules
sequana/rules/Taxonomy/kraken/kraken.rules
sequana/rules/Utils/__init__.py
sequana/rules/Utils/dynamic_copy/dynamic_copy.rules
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
sequana/rules/Variant_caller/freebayes/freebayes.rules
sequana/rules/Variant_caller/freebayes_bcf_filter/freebayes_bcf_filter.rules
sequana/rules/Variant_caller/freebayes_vcf_filter/freebayes_vcf_filter.rules
sequana/rules/Variant_caller/joint_freebayes/joint_freebayes.rules
sequana/rules/Variant_caller/joint_freebayes_vcf_filter/joint_freebayes_vcf_filter.rules
sequana/rules/bam_analysis/bam_analysis.rules
sequana/rules/bam_quality_filter/bam_quality_filter.rules
sequana/rules/bwa_bam_to_fastq/bwa_bam_to_fastq.rules
sequana/rules/bwa_index/bwa_index.rules
sequana/rules/bwa_mem_dynamic/bwa_mem_dynamic.rules
sequana/rules/codecs/__init__.py
sequana/rules/codecs/bam_to_fasta/bam_to_fasta.rules
sequana/rules/codecs/bz2_to_dsrc/bz2_to_dsrc.rules
sequana/rules/codecs/bz2_to_fastq/bz2_to_fastq.rules
sequana/rules/codecs/bz2_to_gz/bz2_to_gz.rules
sequana/rules/codecs/dsrc_to_bz2/dsrc_to_bz2.rules
sequana/rules/codecs/dsrc_to_fastq/dsrc_to_fastq.rules
sequana/rules/codecs/dsrc_to_gz/dsrc_to_gz.rules
sequana/rules/codecs/fastq_to_bz2/fastq_to_bz2.rules
sequana/rules/codecs/fastq_to_dsrc/fastq_to_dsrc.rules
sequana/rules/codecs/fastq_to_gz/fastq_to_gz.rules
sequana/rules/codecs/gz_to_bz2/gz_to_bz2.rules
sequana/rules/codecs/gz_to_dsrc/gz_to_dsrc.rules
sequana/rules/codecs/gz_to_fastq/gz_to_fastq.rules
sequana/rules/copy_multiple_files/copy_multiple_files.rules
sequana/rules/deeptools/__init__.py
sequana/rules/deeptools/BamPEFragmentSize/BamPEFragmentSize.rules
sequana/rules/deeptools/bamCoverage/bamCoverage.rules
sequana/rules/deeptools/multiBamSummary/multiBamSummary.rules
sequana/rules/deeptools/plotCorrelation/plotCorrelation.rules
sequana/rules/deeptools/plotCoverage/plotCoverage.rules
sequana/rules/digital_normalisation/digital_normalisation.rules
sequana/rules/fastq_sampling/fastq_sampling.rules
sequana/rules/fastq_stats_dynamic/fastq_stats_dynamic.rules
sequana/rules/fastqc_dynamic/fastqc_dynamic.rules
sequana/rules/feature_counts/feature_counts.rules
sequana/rules/format_contigs/format_contigs.rules
sequana/rules/igvtools/igvtools.rules
sequana/rules/indel_realigner/indel_realigner.rules
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/scripts/vcf_filter.py
sequana/sphinxext/__init__.py
sequana/sphinxext/snakemakerule.py
sequana/utils/__init__.py
sequana/utils/config.py
sequana/utils/datatables_js.py