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Welcome to the sgRNAble wiki

sgRNAble is a CRISPR-Cas9 single guide RNA (sgRNA) design tool, for high-thoughput sgRNA design in non-model prokaryotic strains or user-defined host genomes.

Basic Usage

 sgrnable -t TARGET_SEQUENCE.fasta -g GENOME_SEQUENCE.fasta
          [GENOME_SEQUENCE.fasta ...] [-a AZIMUTH_CUTOFF]
          [-c COPY_NUMBER [COPY_NUMBER ...]]
          [-o OUTPUT_DIR] [-p PURPOSE]
          [-th NUM_THREADS] [-m MAX_MEMORY] [-v]

Documentation

All associated documentation for the current release is accessible in the links below or in the toolbar to the right of the screen.

• Introduction to sgRNAble

  • About sgRNAble - What is sgRNAble?
  • Citation - How should I cite sgRNAble?
  • Contact - Who should I contact in case of issues?

• Installation

  • Installing sgRNAble - How do I install sgRNAble and dependencies?
  • Downloading required files - What files are required to run sgRNAble?
  • Computational requirements - Is my system capable of running sgRNAble?

• Quick start

  • Tutorial on standard sgRNA design - How do I design sgRNAs targeting 1 or multiple genes in my host genome of choice?

• Advanced usage

  • Overview - Overview of advanced sgRNAble applications
  • Genome-wide sgRNA libary design - How can I design a genome-wide sgRNA library?

• Contributing - Contribution guide for sgRNAble developers.

• Glossary - Concept Definitions.

References

Farasat, I., & Salis, H. M. (2016). A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation. PLOS Computational Biology, 12(1), e1004724. doi:10.1371/journal.pcbi.1004724

Doench, J. G., Fusi, N., Sullender, M., Hegde, M., Vaimberg, E. W., Donovan, K. F., . . . Root, D. E. (2016). Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nature biotechnology, 34, 184. doi:10.1038/nbt.3437