The gamtools plot_np tool is used to plot the sequencing coverage and the window calling output for a single NP over the whole genome. It can be very useful as a quick quality control, as NPs that have been sequenced correctly display a characteristic pattern of coverage, with many large regions (up to whole chromosomes) displaying very low coverage.

Plotting the coverage for an NP requires three files, a bigwig file made from the raw sequencing data, a bed file containing the positive windows and a file containing a list of chromosomes and their lengths in bp (a genome file).

Usage and option summary


gamtools plot_np -w BIGWIG_FILE -b BED_FILE
                 -g GENOME_FILE -o OUTPUT_FILE