Fig. 1

Overview of GUIDEseq Analysis Workflow. Schematic representation of the GUIDEseq analysis pipeline. Input files required for preprocessing and GUIDEseq package are represented by annotated color arrows. First, Preprocessing Utilities are supplied to demultiplex the Illumina FASTQ files based on the index information and map the sequence files to the reference genome. This generates the experimental input files (BAM and UMI files) needed for the GUIDEseq pipeline, which are supplemented with information on the guide RNA (gRNA) and PAM element by the end-user. Key steps carried out by the algorithms within the GUIDEseq pipeline are indicated under the different headers. Details about the R-based commands and variables used within GUIDEseq are presented in the Use Cases within the main text, and are described in full in the Installation and Usage Section [see Additional file 1] and in the manual pages associated with the program