About CRISpy-pop


CRISpy-pop is a web application that generates and filters guide RNA sequences for CRISPR/Cas9 genome editing. This tool focuses on generating guide RNA sequences for Yeast and Bacterial species used in bioenergy research. This tool supports a 1011 genome Saccharomyces cerevisiae strain set as well as a 167 strain set of S. cerevisiae isolates


CRISpy-pop utilizes the following open-source software tools:



Cas-OFFinder

Bae S., Park J. & Kim J.-S. Cas-OFFinder: A fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30, 1473-1475 (2014).

sgRNA Scorer

Chari R, Yeo N, Chavez A, Church GM (2017). sgRNA Scorer 2.0 – a species independent model to predict CRISPR/Cas9 activity. ACS Synthetic Biology. Accepted.

CasFinder

Aach J, Mali P, Church GM (2014). CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes. BioRxiv.


[v0.1.10] - 2021-04-02

Fixed (1 changes)

  • sanitized inputs on command line pipeline

Changed (1 changes)

  • updated gems and js libraries

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog

Versioning is loosely based on Semantic Versioning

  • Major - large feature changes
  • Minor - bi-weekly update
  • Patch - mid-week update

[0.2.0] - 2020-10-09

Added

  • Honeybadger Error Tracking

[0.1.9] - 2020-09-25

Fixed

  • Issue with custom target searches throwing error

[0.1.8] - 2020-08-03

Added

  • PAM options
  • Strain set identifier to strain listings

Removed

  • ZM4 from GLBRC strain set

Changed

  • clean up strain coverage listing

[0.1.7] - 2020-05-21

  • removed gene alias name
  • change "% Activity" to "Activity Score"

[0.1.6] - 2020-04-13

  • Updated logo
  • Updated site title

Changed

  • Changed name of application to CRISpy-pop
  • New logo

[0.1.5] - 2020-04-08

Changed

  • Changed name of application to CRISpy-pop
  • New logo

[0.1.0] - 2019-12-11

Added

  • Enable python pipeline
  • Rework UI in React.js

[0.0.1] - 2019-10-07

Added

  • /api/v1/status endpoint
  • basic layout

Initial Application Configuration

  • Lograge Logging Configuration
  • GLBRC Auth
  • ESLint
  • Rubocop
  • RSpec
  • Brakeman
  • Bundler-Audit
  • Webpacker
  • React
  • Foreman Configuration