ENCoRE: a lightweight software for CRISPR screens

As CRISPR/Cas9 mediated screens with pooled sgRNA libraries in somatic cells become increasingly established, an unmet need for rapid and accurate companion informatics tools has emerged. We have developed a lightweight standalone software to easily manipulate raw large next generation sequencing datasets derived from such screens into informative relational context with graphical support. The advantages of the software entitled ENCoRE (Easy NGS-to-Gene CRISPR REsults) include platform independence, local and fast multithreaded processing, simple graphical workflow, data pre-processing and gene mapping with custom library import. This software enables bench scientists without access to informatic cores to rapidly interpret results from large scale experiments resulting from CRISPR/Cas9 library screens.

To use ENCoRE you must have JAVA software installed on your desktop machine. Instructions to install the software are found below:
First you must download the JAVA Runtime environment (version 8 or higher) and then install this program (as an administrator) on your computer:
JAVA Runtime environment for Windows operating system (also available for other operating systems from the Oracle web page).

After you have installed the JAVA Runtime environment you can download the executable ENCoRE jar file.                                                     

The documentation for the ENCoRE program can be found here: ENCoRE_Quick_Guide.pdf

ENCoRE is an open source software and can be redistributed under the terms of the GNU license: GNU_GENERAL_PUBLIC_LICENSE.docx

A list of libraries and their license agreements used by ENCoRE is available under this link: ENCoRE_embedded_libraries_with_license_information.xlsx

The source code of ENCoRE was exported from Eclipse Java Mars Edition as an Archive File in zip format: ENCoRE.zip

FASTQ Filter

We demonstrate the capabilities of ENCoRE to interrogate meaningful results from an in vitro viability screen using Tumor Necrosis Factor-alpha in fibroblast cells of mouse. Genomic DNA was isolated from selected pools and sequencing was carried out on an Ion Torrent P1 chip. By using the FASTQ Filter Module (FFM) of ENCoRE, we identified all single reads contained in the FASTQ file. Sequencing reads were then trimmed directly after the search sequence ‘gaaacaccg’ at 3’ ends consisting of 19 bp also in the FFM module.

Example input files and a sequence trimming workflow wlf file which can be imported into the FASTQ Filter of ENCoRE can be downloaded for testing via the following links:

TNFa_treated.fastq (~4GB)
Control_Library.fastq (~15GB)

Sample input file with reduced size of read counts can be found via these links:

Sample_TNFa_treated.fastq (~1.2GB)
Sample_Control_Library.fastq (~1GB)


The filtered example input files by the workflow described above can be used together with the annotation csv file from Kosuke (Koike-Yusa, 2014 Nat Biotechnol 32(3): 267-273) to calculate statistics in the CRISPR Report module of ENCoRE and to compare the counts of individual guides from the TNFalpha treated  library with the total starting library. The filtered files can be exported from ENCoRE. In addition, we provide these files for testing together with reference file from Kosuke:

FILTERED_Tnfa_treated.fastq (~600MB)
FILTERED_Control_Library.fastq (~2GB)

Filtered sample input file with reduced size of read counts can be found via these links: FILTERED_Sample_TNFa_treated.fastq (~200MB)
FILTERED_Sample_Control_Library.fastq (~155MB)

Installation Instructions

It is recommended that all files are opened from a local hard drive (see ENCoRE_Quick_Guide.pdf for more details). Further, a computer with at least 4 GB RAM, two CPU's (cores) and 64bit processor is recommended for executing ENCoRE.