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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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