Gepard

Genome Pair Rapid Dotter (gepard)

Table of Contents

• Introduction
• Installation
  • Using Docker
  • Using Conda
• Cite

Introduction

Gepard provides a user-friendly, interactive application for the quick creation of dotplots. It utilizes suffix arrays to reduce the time complexity of dotplot calculation to Theta(m*log n). A client-server mode, which is a novel feature for dotplot creation software, allows the user to calculate dotplots and color them by functional annotation without any prior downloading of sequence or annotation data. A detailed description of how to use gepard can be found in the tutorial.html file.

Installation

Using Docker

First you must have Docker installed and running.
Secondly have look at the availabe Gepard containers at https://quay.io/repository/biocontainers/gepard?tab=tags.
Then:

# get the chosen AGAT version
docker pull quay.io/biocontainers/gepard:2.1.0--hdfd78af_0
# use an AGAT's tool e.g. agat_convert_sp_gxf2gxf
docker run quay.io/biocontainers/gepard:2.1.0--hdfd78af_0 gepardcmd

Using Conda

  # create gepard environment and install gepard
  conda create --name gepard -c bioconda gepard
  # activate gepard environment
  conda activate gepard
  # run gepard
  gepardcmd

Cite

Jan Krumsiek, Roland Arnold, Thomas Rattei, Gepard: a rapid and sensitive tool for creating dotplots on genome scale, Bioinformatics, Volume 23, Issue 8, 15 April 2007, Pages 1026–1028, https://doi.org/10.1093/bioinformatics/btm039