CRISPR-Clue is a web-based bioinformatics tool and wet-lab pipeline for the parallel construction of multiple, custom sgRNA libraries. If you want to clone customized sgRNA libraries Clue provides a frame-work to design and clone these libraries in a fast, efficient and parallel way without the need for any bioinformatic knowledge. You simply start by designing as many sgRNA libraries as you wish, just providing lists of gene names in the columns of a spreadsheet. This file is submitted to Clue and converted into an Oligo Pool where each sgRNA sub-library gets a specific adapter sequence (AdpX). Additionally, Clue adds common adapter sequences (A and B) for amplification of the entire Oligo Pool and Gibson cloning to your favorite sgRNA expression vector.
Clue accepts two different formats of input files, the gene or sequence format. In the gene format each column of your spreadsheet contains one sgRNA library, starting with library name, species (human or murine), type of CRISPR library (ko, kd, act for CRISPRko/i/a, respectively), followed by gene names.
In the sequence format you can directly provide sgRNA sequences, thereby already defining species and type of CRISPR system. Here, one library is provided in 2 columns with the first column holding sgRNA IDs and the second column holding the name of your library and the sgRNA sequences.