SeamlessF5 adds useful missing features for the easier transition to Oxford Nanopore Technologies' new multi-read FAST5 format.
SeamlessF5 can be installed using pip for Python 3.5+.
pip install seamlessf5
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
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. Just add
sf5_
before your old command lines.
sf5_read_fast5basecaller.py -i multiread-fast5-dir ...