├── .gitignore ├── LICENSE.txt ├── README.md ├── lib ├── SAMtools │ ├── __init__.py │ ├── ace2sam.exe │ ├── bcftools.exe │ ├── bgzip.exe │ ├── htsfile.exe │ ├── maq2sam-long.exe │ ├── maq2sam-short.exe │ ├── md5fa.exe │ ├── md5sum-lite.exe │ ├── msys-2.0.dll │ ├── msys-ncursesw6.dll │ ├── msys-z.dll │ ├── samtools.exe │ ├── tabix.exe │ └── wgsim.exe ├── __init__.py ├── alg_routines_unix.py ├── alg_routines_win.py ├── alignment.py ├── colored_log.py ├── fast5_reader.py ├── fastqgen.py ├── fastqmpi.py ├── fastqparser.py ├── logging_module.py ├── minimap2 │ ├── .DS_Store │ ├── __init__.py │ ├── __init__.pyc │ ├── minimap2.exe │ ├── msys-2.0.dll │ └── msys-z.dll ├── multi_read_fast5_reader.py ├── pypore.py ├── seq_routines.py └── seqstats.py ├── readme_data ├── MPI_Win.md ├── MPI_mac.md ├── OpenMPIUnix.md ├── Seq_summary.gif ├── alignment_summary.gif └── pore_map.gif └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/README.md -------------------------------------------------------------------------------- /lib/SAMtools/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /lib/SAMtools/ace2sam.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/SAMtools/ace2sam.exe -------------------------------------------------------------------------------- /lib/SAMtools/bcftools.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/SAMtools/bcftools.exe -------------------------------------------------------------------------------- /lib/SAMtools/bgzip.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/SAMtools/bgzip.exe -------------------------------------------------------------------------------- /lib/SAMtools/htsfile.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/SAMtools/htsfile.exe -------------------------------------------------------------------------------- /lib/SAMtools/maq2sam-long.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/SAMtools/maq2sam-long.exe -------------------------------------------------------------------------------- /lib/SAMtools/maq2sam-short.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/SAMtools/maq2sam-short.exe -------------------------------------------------------------------------------- /lib/SAMtools/md5fa.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/SAMtools/md5fa.exe -------------------------------------------------------------------------------- /lib/SAMtools/md5sum-lite.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/SAMtools/md5sum-lite.exe -------------------------------------------------------------------------------- /lib/SAMtools/msys-2.0.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/SAMtools/msys-2.0.dll -------------------------------------------------------------------------------- /lib/SAMtools/msys-ncursesw6.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/SAMtools/msys-ncursesw6.dll -------------------------------------------------------------------------------- /lib/SAMtools/msys-z.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/SAMtools/msys-z.dll -------------------------------------------------------------------------------- /lib/SAMtools/samtools.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/SAMtools/samtools.exe -------------------------------------------------------------------------------- /lib/SAMtools/tabix.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/SAMtools/tabix.exe -------------------------------------------------------------------------------- /lib/SAMtools/wgsim.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/SAMtools/wgsim.exe -------------------------------------------------------------------------------- /lib/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /lib/alg_routines_unix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/alg_routines_unix.py -------------------------------------------------------------------------------- /lib/alg_routines_win.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/alg_routines_win.py -------------------------------------------------------------------------------- /lib/alignment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/alignment.py -------------------------------------------------------------------------------- /lib/colored_log.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/colored_log.py -------------------------------------------------------------------------------- /lib/fast5_reader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/fast5_reader.py -------------------------------------------------------------------------------- /lib/fastqgen.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/fastqgen.py -------------------------------------------------------------------------------- /lib/fastqmpi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/fastqmpi.py -------------------------------------------------------------------------------- /lib/fastqparser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/fastqparser.py -------------------------------------------------------------------------------- /lib/logging_module.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/logging_module.py -------------------------------------------------------------------------------- /lib/minimap2/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/minimap2/.DS_Store -------------------------------------------------------------------------------- /lib/minimap2/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /lib/minimap2/__init__.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/minimap2/__init__.pyc -------------------------------------------------------------------------------- /lib/minimap2/minimap2.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/minimap2/minimap2.exe -------------------------------------------------------------------------------- /lib/minimap2/msys-2.0.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/minimap2/msys-2.0.dll -------------------------------------------------------------------------------- /lib/minimap2/msys-z.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/minimap2/msys-z.dll -------------------------------------------------------------------------------- /lib/multi_read_fast5_reader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/multi_read_fast5_reader.py -------------------------------------------------------------------------------- /lib/pypore.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/pypore.py -------------------------------------------------------------------------------- /lib/seq_routines.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/seq_routines.py -------------------------------------------------------------------------------- /lib/seqstats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/lib/seqstats.py -------------------------------------------------------------------------------- /readme_data/MPI_Win.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/readme_data/MPI_Win.md -------------------------------------------------------------------------------- /readme_data/MPI_mac.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/readme_data/MPI_mac.md -------------------------------------------------------------------------------- /readme_data/OpenMPIUnix.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/readme_data/OpenMPIUnix.md -------------------------------------------------------------------------------- /readme_data/Seq_summary.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/readme_data/Seq_summary.gif -------------------------------------------------------------------------------- /readme_data/alignment_summary.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/readme_data/alignment_summary.gif -------------------------------------------------------------------------------- /readme_data/pore_map.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/readme_data/pore_map.gif -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rsemeraro/PyPore/HEAD/setup.py --------------------------------------------------------------------------------