AGouTI - flexible Annotation of Genomic and Transcriptomic Intervals

Abstract Summary The recent development of high-throughput workflows in genomics and transcriptomics revealed that efficient annotation is essential for effective data processing and analysis. Although a variety of tools dedicated to this purpose is available, their functionality is limited. Here, we present AGouTI – a universal tool for flexible annotation of any genomic or transcriptomic coordinates using known genomic features deposited in different publicly available databases in the form of GTF or GFF files. In contrast to currently available tools, AGouTI is designed to provide a flexible selection of genomic features overlapping or adjacent to annotated intervals, can be used on custom column-based text files obtained from different data analysis pipelines, and supports operations on transcriptomic coordinate systems. Availability and Implementation AGouTI was implemented using Python 3 and is freely available on GitHub ( https://github.com/zywicki-lab/agouti ), from the Python Package Index ( https://pypi.org/project/AGouTI/ ) or Anaconda Cloud ( https://anaconda.org/bioconda/agouti ). We also provide a Galaxy wrapper available from the Galaxy Tool Shed ( https://toolshed.g2.bx.psu.edu/view/janktoolshed/agouti/c204da8f836d ). Supplementary information Supplementary Data are available at Publisher site online. Files for replicating the use-case scenario described in Supplementary Data are available at Zenodo: https://doi.org/10.5281/zenodo.7317210 . Contact Marek.Zywicki@amu.edu.pl