LICENSE.md
README.md
setup.py
accusnv/CNN_pred.py
accusnv/Snakefile
accusnv/__init__.py
accusnv/__main__.py
accusnv/accusnv_downstream.py
accusnv/accusnv_main.py
accusnv/accusnv_snakemake.py
accusnv/cli.py
accusnv/config.yaml
accusnv/downstream.py
accusnv/experiment_info.yaml
accusnv/new_snv_script.py
accusnv/slurm_status_script.py
accusnv.egg-info/PKG-INFO
accusnv.egg-info/SOURCES.txt
accusnv.egg-info/dependency_links.txt
accusnv.egg-info/entry_points.txt
accusnv.egg-info/requires.txt
accusnv.egg-info/top_level.txt
accusnv/CNN_models/checkpoint_best_3conv.pt
accusnv/CNN_models/checkpoint_best_3conv_imbalance.pt
accusnv/modules/__init__.py
accusnv/modules/build_SNP_Tree.py
accusnv/modules/build_SNP_Tree_v202504.py
accusnv/modules/snv_module_recoded.py
accusnv/modules/snv_module_recoded_new.py
accusnv/modules/snv_module_recoded_with_dNdS.py
accusnv/scripts/annotation_orthologs_inference.py
accusnv/scripts/basic_snakemake_functions.py
accusnv/scripts/bowtie2qc.py
accusnv/scripts/bracken
accusnv/scripts/bracken-build
accusnv/scripts/build_candidate_mutation_table.py
accusnv/scripts/build_candidate_mutation_table_40features.py
accusnv/scripts/combine_positions.py
accusnv/scripts/dry_run.sh
accusnv/scripts/fq2fa_sed.sh
accusnv/scripts/gus_helper_functions.py
accusnv/scripts/install_subenv.sh
accusnv/scripts/local_run.sh
accusnv/scripts/mergeFQ_runSPAdes.py
accusnv/scripts/pileup2diversity.py
accusnv/scripts/run_snakemake.slurm
accusnv/scripts/run_snakemake_depth_rerun.sh
accusnv/scripts/run_snakemake_repeat.slurm
accusnv/scripts/run_snakemake_vp.slurm
accusnv/scripts/sed_nl.sh
accusnv/scripts/variants2positions.py
accusnv/scripts/vcf2quals_snakemake.py
accusnv/scripts/__pycache__/gus_helper_functions.cpython-311.pyc
accusnv/scripts/__pycache__/gus_helper_functions.cpython-312.pyc
accusnv/scripts/__pycache__/gus_helper_functions.cpython-37.pyc
accusnv/scripts/src/Makefile
accusnv/scripts/src/ctime.cpp
accusnv/scripts/src/ctime.h
accusnv/scripts/src/ctime.o
accusnv/scripts/src/est_abundance.py
accusnv/scripts/src/generate_kmer_distribution.py
accusnv/scripts/src/kmer2read_distr
accusnv/scripts/src/kmer2read_distr.cpp
accusnv/scripts/src/kmer2read_distr.o
accusnv/scripts/src/kmer2read_headers.h
accusnv/scripts/src/kraken_processing.cpp
accusnv/scripts/src/kraken_processing.h
accusnv/scripts/src/kraken_processing.o
accusnv/scripts/src/taxonomy.cpp
accusnv/scripts/src/taxonomy.h
accusnv/scripts/src/taxonomy.o