A tool for studying repetitive DNA dynamics using low-coverage, short-read data. RepeatProfiler automates generation and visualization of repeat profiles from low-coverage sequence data and allows statistical comparison of profile attributes. The pipeline maps reads to consensus sequences of one or more repeat of interest, generates visually enhanced read depth/copy number profiles for each repeat, and facilitates comparison across profiles within and among samples. Output enables standardized visualization of profiles, comparative analysis of profile shape within and among user-defined groups, and prepares input files for phylogenetic analysis signal arising from variants within repeat profiles. RepeatProfiler is developed specifically to facilitate study of repetitive DNA dynamics over short evolutionary time scales in groups with limited genomic resources; however, it may be useful in any application where extracting signal from repetitive sequences is useful.

Features

• Facilitates data visualization of repeat profiles using short-read data
• Produces publication-quality graphs that simplify visual comparison of profiles
• Produces summary statistics related to repeat abundance
• Conducts comparative analysis of profile shape between and within user-specified groups
• Enables comparative study of variation within repeats through phylogenetic analysis