SWOffinder

SWOffinder is a method based on Smith-Waterman alignment to find all off-target sites up to some edit distance efficiently. We implemented a trace-back method to find off-target sites under versatile criteria, such as separate limits on the number of insertions, deletions, and mismatches.

Usage

1. First, you need to compile and build the SmithWatermanOffTarget package: javac -d bin SmithWatermanOffTarget/*.java
2. To search, execute the command line java -cp bin SmithWatermanOffTarget.SmithWatermanOffTargetSearchAlign <Genome reference path> <sgRNA list path> <Output path prefix> <maxE> <maxM> <maxMB> <maxB> <Threads> <Best in-a-window> <Best in-a-window size> <PAM> <Allow PAM edits>

The arguments specification:

1. Genome reference path: The path of the FASTA file containing the Genome reference.
2. sgRNA list: The path of a text file containing a list of sgRNAs with their PAM (see sgRNAs.txt file for example).
3. Output path prefix: The path for the output files with file prefix. files are saved in "CSV" format.
4. maxE: Max edits allowed (integer).
5. maxM: Max mismatches allowed without bulges (integer).
6. maxMB: Max mismatches allowed with bulges (integer).
7. maxB: Max bulges allowed (integer).
8. Threads: The number of threads to use for the run (integer).
9. Best in-a-window: Flag whether to choose the best off-target site in a window or not (true or false).
10. Best in-a-window size: The window size for choosing the best in a window (integer). Please insert even if Best in-a-window is false.
11. PAM: The PAM sequence (for example, NGG).
12. Allow PAM edits: Flag whether to allow PAM edits or not (true or false).

Requirements:

The code was tested with openjdk version "17.0.3"