.travis.yml
LICENSE
README.rst
install.sh
requirements.txt
setup.cfg
setup.py
tests.sh
upload_pypi.sh
RNFtools.egg-info/PKG-INFO
RNFtools.egg-info/SOURCES.txt
RNFtools.egg-info/dependency_links.txt
RNFtools.egg-info/not-zip-safe
RNFtools.egg-info/pbr.json
RNFtools.egg-info/requires.txt
RNFtools.egg-info/top_level.txt
bin/rnf-join-fq.py
docs/Makefile
docs/conf.py
docs/getting_started.rst
docs/index.rst
docs/make.bat
docs/reference.rst
docs/resources.rst
docs/tutorial.rst
docs/reference/01_mishmash.rst
docs/reference/02_lavender.rst
docs/reference/03_rnf_format.rst
docs/reference/04_other_tools.rst
docs/resources/developers.rst
docs/resources/faq.rst
docs/resources/read_simulators.rst
docs/tutorial/00_installation.rst
docs/tutorial/01_first_snakefile.rst
docs/tutorial/02_simulation.rst
docs/tutorial/03_evaluation.rst
examples/.gitignore
examples/other_examples/all_simulators_example/Snakefile
examples/other_examples/rnf_paper_example/bams/Snakefile
examples/other_examples/rnf_paper_example/report/Snakefile
examples/tutorial/01_first_snakefile/Snakefile
examples/tutorial/02_simulation/01_simple_simulation/Snakefile
examples/tutorial/02_simulation/02_paired_end_reads/Snakefile
examples/tutorial/02_simulation/03_different_simulator/Snakefile
examples/tutorial/02_simulation/04_more_genomes/Snakefile
examples/tutorial/02_simulation/05_more_samples/Snakefile
examples/tutorial/02_simulation/06_nonstandard_parameters/Snakefile
examples/tutorial/03_evaluation/01_simple_evaluation/bams/Snakefile
examples/tutorial/03_evaluation/01_simple_evaluation/report/Snakefile
examples/tutorial/03_evaluation/02_single_end/bams/Snakefile
examples/tutorial/03_evaluation/02_single_end/report/Snakefile
examples/tutorial/03_evaluation/03_paired_end/bams/Snakefile
examples/tutorial/03_evaluation/03_paired_end/report/Snakefile
rnftools/__init__.py
rnftools/include_all.snake
rnftools/lavender/__init__.py
rnftools/lavender/bam.py
rnftools/lavender/lavender.snake
rnftools/lavender/panel.py
rnftools/lavender/report.py
rnftools/mishmash/__init__.py
rnftools/mishmash/_source.py
rnftools/mishmash/artIllumina.py
rnftools/mishmash/cuReSim.py
rnftools/mishmash/dwgSim.py
rnftools/mishmash/mishmash.snake
rnftools/mishmash/sample.py
rnftools/mishmash/wgSim.py
rnftools/rnfformat/__init__.py
rnftools/rnfformat/formatter.py
rnftools/rnfformat/readTuple.py
rnftools/rnfformat/segment.py