An experimental, long read genome-assembler that leverages k-mer pairs along with distance information to map error-prone reads with high fidelity. This application is very much a work in progress, and consists of a simple command line interface for robustly approximating a Jaccard index between two strings. More to come...
- Python 2.7
- Cython
- Numpy
$ git clone https://github.com/davisem/spire.git
$ cd spire
$ virtualenv venv
$ source venv/bin/activate
$ pip install cython numpy
$ python setup.py build_ext --inplace
$ python spire.py -q ATCGGATCGAATCG -r ATCGATCGATCGATCG -k 3 -m deep -n 300
| Option | Description |
|---|---|
| help | Display help message |
| reference | A reference string to search against |
| query_string | A string to compare to the reference |
| n_hashing_functions | Number of random hashing functions to use |
| word_size | Word size with which input strings will be enumerated |
| mode | [fast, deep] Whether to enumerate kmers (fast) or kmer-pairs (deep) |
Original concept by Hamidreza Chitsaz. Implemented by Chris Dean, Eric Davis, and Patrick Hagarty
Feel free to send me an email at emdavis48 AT gmail DOT com