├── LICENSE ├── README.md ├── cluster_trans_new.py ├── docker └── Dockerfile ├── filter_reads_bwa_efficient.py ├── grid_search_on_validation_dataset.txt ├── process_grid_search.py ├── run_kraken_vifi_container.py ├── run_kraken_vifi_pipeline.py └── test ├── human_chr_list.txt ├── test_fastvifi.sh ├── test_reads_1.fq └── test_reads_2.fq /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sara-javadzadeh/FastViFi/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sara-javadzadeh/FastViFi/HEAD/README.md -------------------------------------------------------------------------------- /cluster_trans_new.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sara-javadzadeh/FastViFi/HEAD/cluster_trans_new.py -------------------------------------------------------------------------------- /docker/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sara-javadzadeh/FastViFi/HEAD/docker/Dockerfile -------------------------------------------------------------------------------- /filter_reads_bwa_efficient.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sara-javadzadeh/FastViFi/HEAD/filter_reads_bwa_efficient.py -------------------------------------------------------------------------------- /grid_search_on_validation_dataset.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sara-javadzadeh/FastViFi/HEAD/grid_search_on_validation_dataset.txt -------------------------------------------------------------------------------- /process_grid_search.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sara-javadzadeh/FastViFi/HEAD/process_grid_search.py -------------------------------------------------------------------------------- /run_kraken_vifi_container.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sara-javadzadeh/FastViFi/HEAD/run_kraken_vifi_container.py -------------------------------------------------------------------------------- /run_kraken_vifi_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sara-javadzadeh/FastViFi/HEAD/run_kraken_vifi_pipeline.py -------------------------------------------------------------------------------- /test/human_chr_list.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sara-javadzadeh/FastViFi/HEAD/test/human_chr_list.txt -------------------------------------------------------------------------------- /test/test_fastvifi.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sara-javadzadeh/FastViFi/HEAD/test/test_fastvifi.sh -------------------------------------------------------------------------------- /test/test_reads_1.fq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sara-javadzadeh/FastViFi/HEAD/test/test_reads_1.fq -------------------------------------------------------------------------------- /test/test_reads_2.fq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sara-javadzadeh/FastViFi/HEAD/test/test_reads_2.fq --------------------------------------------------------------------------------