Off-Target is a short-string (<50bp) search query tool which maps queries to hits with high mismatches or Insertion Deletions (InDels) with a default setting of 1 mismatch per 3 nucleotides.

Whilst the algorithm is constantly being updated and a C version is under production, a brief explanation behind Off-Target algorithm will be updated soon! (Stay Tuned!)

Installation:

git clone https://github.com/chewlabSB2/OffTarget.git
cd OffTarget 
python setup.py install

OffTarget -r References.fasta -q Query.fasta -p Test -m 8 --threads 2 -d

Off-Target output is according to SAM file conventions. A sample of the results can be found here.