title: CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries.
abstract: BACKGROUND
  Genetic screens using CRISPR/Cas9 are a powerful method for the functional analysis of genomes.
  
  
  RESULTS
  Here we describe CRISPR library designer (CLD), an integrated bioinformatics application for the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated genomes. CLD is suitable for the design of libraries using modified CRISPR enzymes and targeting non-coding regions. To demonstrate its utility, we perform a pooled screen for modulators of the TNF-related apoptosis inducing ligand (TRAIL) pathway using a custom library of 12,471 sgRNAs.
  
  
  CONCLUSIONS
  CLD predicts a high fraction of functional sgRNAs and is publicly available at https://github.com/boutroslab/cld.
authors.affiliation: Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Heigwer
authors.affiliation: Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120, Germany.|Department of Medicine II, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
authors.forename: Tianzuo
authors.initials: T
authors.lastname: Zhan
authors.affiliation: Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120, Germany.
authors.forename: Marco
authors.initials: M
authors.lastname: Breinig
authors.affiliation: Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Winter
authors.affiliation: Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120, Germany.
authors.forename: Dirk
authors.initials: D
authors.lastname: Brügemann
authors.affiliation: Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120, Germany.
authors.forename: Svenja
authors.initials: S
authors.lastname: Leible
authors.affiliation: Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120, Germany. m.boutros@dkfz.de.
authors.forename: Michael
authors.identifier: http://orcid.org/0000-0002-9458-817X
authors.initials: M
authors.lastname: Boutros
mesh_terms: D000818:Animals; D064113:CRISPR-Cas Systems; D019295:Computational Biology / Q000379:methods; D015723:Gene Library; D006801:Humans; D000094704:RNA, Guide, CRISPR-Cas Systems; D012984:Software; D053221:TNF-Related Apoptosis-Inducing Ligand / Q000235:genetics*
chemical_list: D000094704:RNA, Guide, CRISPR-Cas Systems; D053221:TNF-Related Apoptosis-Inducing Ligand
keywords: Bioinformatics; CRISPR/Cas9; Functional genomics; Pooled screens; sgRNA design