A program used to find indels from next-genearation sequencing data on target gene edited by CRISPR/Cas9 and then calculate the on-target efficiency. The indel information will be presented as figures plotted by matplotlib, a module of python. You can also use other software, like OriginLab, to plot indel data by yourself.

Indel-Finder uses Nucleotide-Nucleotide BLAST 2.4.0+ to find reads position and do local alignment and then processes the blast result to get indel and calculate the on-target efficiency.
Python2.7

Indel-Finder use numpy module and matplotlib module.
User can install them by using pip:

pip install numpy
pip install matplotlib

git clone https://github.com/TuanjieNew/Indel-Finder.git

python indel_finder.py -r ./sample/crr5ref.fa -t ./sample/target1.fa -1 ./sample/1_S1_L001_R1_001.fastq -2 ./sample/1_S1_L001_R2_001.fastq -o ./

-h   show this help message and exit.

-r   file name of reference file, required. The file is fasta format.
-t   file name of target sequence, required. The file is fasta format.
-1   file name of read1, required. The file is fastq or fastq.gz format.
-2   file name of read2, required. The file is fastq or fastq.gz format.
-o   outpout directories. Default is ./ . The blast results are in cas_temp, indel data in ./_result, figures in ./_figures.

Mosacism index is from Gini–Simpson index used to evaluate the degree of chimera.
A mosacism index close to 1 means a high degree of chimera.
It can be expressed as a transformation of true diversity of order 2:

Indel-Finder is MIT-licensed.