LexicHash

Sequence Similarity Estimation via Lexicographic Comparison of Hashes

For help running LexicHash/MinHash, run the following in LexicHash directory:

python3 run_module.py -h

Example on NCTC1080 dataset:

python3 run_module.py --out ../LH_out --fasta data/NCTC1080/NCTC1080_reads.fasta.gz --n_hash 100 --max_k 32

To install requirements, run

pip install -r requirements.txt

For now, LexicHash cannot deal with sequences with N's.

The groundtruth alignmnent file has the following column format:

1. First read index (zero-based)
2. Second read index (zero-based)
3. Alignment size in base-pairs
4. Second read alignment orientation (+/-)

The output alignmnent file has the following column format:

1. First read index (zero-based)
2. Second read index (zero-based)
3. Alignment score
4. Second read alignment orientation (+/-)