The goal of this project is to be able to efficiently search for subsequences in a genome by following the bowtie tool strategy. It consists in computing an index of the reference sequence using the Burrow-Wheeler (BW) transform and then using an efficient search procedure on the transformed sequence.
Using a Python interpreter:
bw-build.py [-h] [--compress] [--progressive k] infile outfile f
python3 src/bw-build.py cmv.fasta cmv.fasta.idxc 5 --compress
bw-search.py [-h] [--count-only] infile q
python3 src/bw-search.py --count-only data/cmv.fasta.idx ATT
quoc-duong.nguyen