Source Code on GitHub

Softwares Used

Off-Spotter v0.2.2

Official website:

Off-Spotter is designed to identify gRNAs followed by PAM on input and return ALL genomic locations that match a specific gRNA followed by a PAM sequence.

Install steps:
1. Download
2. Run "unzip".
3. Run "make" in unzipped directory.

SSC (Spacer Scoring for CRISPR) v0.1

Official website:

SSC is a tool for predicting sgRNA efficiency from spacer sequences. It supports the applications of optimizing sgRNA libraries in CRISPR/Cas9 knockout or CRISPR/dCas9 inhibition/activation screens.

Install steps:
1. Download SSC0.1.tar.gz.
2. Run "tar -zxvf SSC0.1.tar.gz".
3. Run "make" in unzipped directory.

Necessary Reference Files

Current 10 genomes: hg19, hg38, mm10, bosTau, canFam, danRer, galGal, ratNor, sacCer and susScr.

Each genome has 7 kinds of files:
1. Gennome sequence (.genome)
2. Gene position (.pos)
3. Exon region for on-target (.on.exon)
4. Fasta for Off-Spotter (.fa)
5. Exon region for Off-Spotter (.off.exon)
6. phast conserved element (.phast)
7. gene structure (.structure)

All these files can be downloaded from our FTP server:

Download source of fasta and gtf for the ten genomes:

1) hg19, hg38, mm10 were downloaded from GENCODE database:,

hg19Homo sapiens (Human)GENCODE release19 (hg19)
hg38Homo sapiens (Human)GENCODE release22 (hg38)
mm10Mus musculus (Mouse)GENCODE releaseM4 (mm10)

2) bosTau, canFam, danRer, galGal, ratNor, sacCer and susScr were download from Ensembl database:

bosTauBos taurus (Cow)Ensembl release84 (bosTau6)
canFamCanis lupus familiaris (Dog)Ensembl release84 (canFam3)
danRerDanio rerio (Zebrafish)Ensembl release84 (danRer10)
galGalGallus gallus (Chicken)Ensembl release84 (galGal4)
ratNorRattus norvegicus (Rat)Ensembl release84 (ratNor6)
sacCerSaccharomyces cerevisiae (Yeast)Ensembl release84 (sacCer3)
susScrSus scrofa (Pig)Ensembl release84 (susScr10)

More infomation about reference can be seen in reference_README.txt.