MANIFEST.in
README.rst
setup.cfg
setup.py
pipelines/biomics/README.rst
pipelines/biomics/Snakefile
pipelines/biomics/config.json
pipelines/fix_removal/README.rst
pipelines/fix_removal/Snakefile
pipelines/fix_removal/config.yaml
pipelines/mapping/README.rst
pipelines/mapping/Snakefile
pipelines/mapping/config.yaml
pipelines/variants/README.rst
pipelines/variants/Snakefile
pipelines/variants/config_vc.yaml
pipelines/variants/freebayes_filter.rst
scripts/__init__.py
scripts/fastq_count.py
scripts/fastq_head.py
scripts/sequana.py
sequana/__init__.py
sequana/adapters.py
sequana/bamtools.py
sequana/bedtools.py
sequana/fastq.py
sequana/phred.py
sequana/report_adapter_removal.py
sequana/report_bam.py
sequana/report_cutadapt.py
sequana/report_fastqc.py
sequana/report_main.py
sequana/report_mapping.py
sequana/report_phix.py
sequana/running_median.py
sequana/snaketools.py
sequana/tools.py
sequana/vcf_filter.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/pipelines/__init__.py
sequana/resources/__init__.py
sequana/resources/css/__init__.py
sequana/resources/css/report.css
sequana/resources/data/Coliphage_phiX174.fa
sequana/resources/data/__init__.py
sequana/resources/data/test_10000.fastq.gz
sequana/resources/jinja/__init__.py
sequana/resources/jinja/base.html
sequana/resources/jinja/adapter_removal/__init__.py
sequana/resources/jinja/adapter_removal/index.html
sequana/resources/jinja/bam/__init__.py
sequana/resources/jinja/bam/index.html
sequana/resources/jinja/fastqc/__init__.py
sequana/resources/jinja/fastqc/index.html
sequana/resources/jinja/main/__init__.py
sequana/resources/jinja/main/index.html
sequana/resources/jinja/mapping/__init__.py
sequana/resources/jinja/mapping/index.html
sequana/resources/jinja/phix_contaminant/__init__.py
sequana/resources/jinja/phix_contaminant/index.html
sequana/resources/testing/__init__.py
sequana/rules/__init__.py
sequana/rules/bwa_bam_to_fastq/Snakefile
sequana/rules/bwa_phix/Snakefile
sequana/rules/cleanup/README.rst
sequana/rules/cleanup/Snakefile
sequana/rules/conda/README.rst
sequana/rules/conda/Snakefile
sequana/rules/dag/README.rst
sequana/rules/dag/Snakefile.dag
sequana/rules/fastq_sampling/README.rst
sequana/rules/fastq_sampling/Snakefile
sequana/rules/fastq_sampling/config.yaml
sequana/rules/fastqc/README.rst
sequana/rules/fastqc/Snakefile
sequana/rules/fastqc/config.yaml
sequana/rules/report_phix_removal/Snakefile
test/test_bamtools.py
test/test_bedtools.py
test/test_fastq.py
test/test_phred.py
test/test_report_main.py
test/test_snaketools.py
test/test_tools.py
test/test_vcf_filter.py