/libabea

Adaptive Banded Event Alignment

Primary LanguageCMIT LicenseMIT

Adaptive Banded Event Alignment (abea)

Python library bindings for Adaptive Banded Event Alignment (ABEA) for Nanopore reads. Used for aligning a base-called read to the raw nanopore signal.

Building

pip3 install cython
python3 setup.py build
cp build/lib.*/*.so  ./

Launch a test run

./test.sh

How to use:

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

Usage

See example.py

Acknowledgement

This reuses code and methods from Nanopolish. The event detection code is from Oxford Nanopore's Scrappie basecaller.