Helpers for smoother transitioning to multi-read FAST5 files
Project description
SeamlessF5
SeamlessF5 adds useful missing features that helps making transitions to Oxford Nanopore Technologies's new multi-read FAST5 format.
Installation
SeamlessF5 can be installed using pip for Python 3.5+.
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.
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.
sf5_read_fast5basecaller.py -i multiread-fast5-dir ...
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