Python library bindings for Adaptive Banded Event Alignment (ABEA) for Nanopore reads. Used for aligning a base-called read to the raw nanopore signal.
pip3 install cython
python3 setup.py build
cp build/lib.*/*.so ./
./test.sh
Experimental use on RAGE-seq single-cell data
/usr/bin/time -v python3 -m cProfile -s cumtime motif2sig.py -f demuxed.fastq -s sequencing_summary.txt -p fast5s/ -q ../test_squig.tsv -v 1 -t 0 > test.out.tsv
See example.py
This reuses code and methods from Nanopolish. The event detection code is from Oxford Nanopore's Scrappie basecaller.