Metadata-Version: 2.1
Name: seamlessf5
Version: 0.1
Summary: Helpers for smoother transitioning to multi-read FAST5 files
Home-page: https://github.com/hyeshik/seamlessf5
Author: Hyeshik Chang
Author-email: hyeshik@snu.ac.kr
License: MIT
Download-URL: https://github.com/hyeshik/seamlessf5/releases
Keywords: nanopore,fast5,converter,wrapper
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
Requires-Dist: h5py (>=2.9.0)
Requires-Dist: ont-fast5-api (>=1.0.1)
Requires-Dist: progressbar33 (>=2.4)

# SeamlessF5
SeamlessF5 adds useful missing features that helps making transitions to
Oxford Nanopore Technologies's
[new multi-read FAST5 format](https://community.nanoporetech.com/posts/fast5-file-format-change).

## Installation
SeamlessF5 can be installed using [pip](http://pypi.python.org/pypi/pip)
for Python 3.5+.

```bash
pip install seamlessf5
```

## Conversion from single FAST5 files in `tar` to multi-read FAST5
With the `sf5_single_to_multi_fast5` wrapper, ONT's `single_to_multi_fast5`
becomes capable of loading single-read FAST5 files from `tar` or compressed
`tar` files.

```bash
sf5_single_to_multi_fast5 -i fast5.tar.gz -s save_path --recursive
```

## Running albacore for multi-read FAST5
This package also installs wrappers, `sf5_read_fast5_basecaller.py`,
`sf5_full_1dsq_basecaller.py`, and `sf5_paired_read_basecaller.py` which
enable loading multi-read FAST5 files for ONT's albacore.

```bash
sf5_read_fast5basecaller.py -i multiread-fast5-dir ...
```



