LICENSE
MANIFEST.in
readme.md
setup.py
examples/demo.fastq
examples/demo_db.1.bt2
examples/demo_db.2.bt2
examples/demo_db.3.bt2
examples/demo_db.4.bt2
examples/demo_db.rev.1.bt2
examples/demo_db.rev.2.bt2
kneaddata/__init__.py
kneaddata/bowtie2_discordant_pairs.py
kneaddata/config.py
kneaddata/download_db.py
kneaddata/generate_db.py
kneaddata/knead_data.py
kneaddata/read_count_table.py
kneaddata/read_count_table_concat_pairs.py
kneaddata/run.py
kneaddata/utilities.py
kneaddata.egg-info/PKG-INFO
kneaddata.egg-info/SOURCES.txt
kneaddata.egg-info/dependency_links.txt
kneaddata.egg-info/entry_points.txt
kneaddata.egg-info/not-zip-safe
kneaddata.egg-info/top_level.txt
kneaddata/db_preprocessing/__init__.py
kneaddata/db_preprocessing/convert_rna.py
kneaddata/db_preprocessing/downsample.py
kneaddata/db_preprocessing/fastq_to_fasta.py
kneaddata/db_preprocessing/filter_bugs.py
kneaddata/db_preprocessing/filter_silva.py
kneaddata/db_preprocessing/mergesams.py
kneaddata/db_preprocessing/prefix_human_transcriptome.py
kneaddata/db_preprocessing/reservoir.py
kneaddata/tests/__init__.py
kneaddata/tests/basic_tests.py
kneaddata/tests/cfg.py
kneaddata/tests/functional_tests.py
kneaddata/tests/kneaddata_test.py
kneaddata/tests/utils.py
kneaddata/tests/data/demo.bam
kneaddata/tests/data/demo.fastq
kneaddata/tests/data/demo.fastq.gz
kneaddata/tests/data/demo.sam
kneaddata/tests/data/demo2.fastq
kneaddata/tests/data/demo_matches_sam_and_bam.fastq
kneaddata/tests/data/merge1.fastq
kneaddata/tests/data/merge2.fastq
kneaddata/tests/data/merge3.fastq
kneaddata/tests/data/demo_bowtie2_db/demo_db.1.bt2
kneaddata/tests/data/demo_bowtie2_db/demo_db.2.bt2
kneaddata/tests/data/demo_bowtie2_db/demo_db.3.bt2
kneaddata/tests/data/demo_bowtie2_db/demo_db.4.bt2
kneaddata/tests/data/demo_bowtie2_db/demo_db.rev.1.bt2
kneaddata/tests/data/demo_bowtie2_db/demo_db.rev.2.bt2