Science Score: 13.0%
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○CITATION.cff file
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✓DOI references
Found 2 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (8.7%) to scientific vocabulary
Last synced: 4 months ago
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JSON representation
Repository
Genome Pair Rapid Dotter
Basic Info
- Host: GitHub
- Owner: Juke34
- License: mit
- Language: Java
- Default Branch: master
- Homepage: http://cube.univie.ac.at/gepard
- Size: 9.72 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Fork of univieCUBE/gepard
Created over 4 years ago
· Last pushed over 4 years ago
https://github.com/Juke34/gepard/blob/master/
[](https://anaconda.org/bioconda/gepard)
[](https://anaconda.org/bioconda/gepard)
[](https://anaconda.org/bioconda/gepard)
[](https://conda.anaconda.org/bioconda)
Gepard
===========================
Genome Pair Rapid Dotter (gepard)
## Table of Contents
* [Introduction](#introduction)
* [Installation](#installation)
* [Using Docker](#using-docker)
* [Using Conda](#using-conda)
* [Cite](#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.
## Installation
### Using Docker
First you must have [Docker](https://docs.docker.com/get-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 10261028, https://doi.org/10.1093/bioinformatics/btm039
Owner
- Name: Jacques Dainat
- Login: Juke34
- Kind: user
- Location: Montpellier, France
- Company: IRD
- Website: https://www.researchgate.net/profile/Jacques-Dainat-2
- Twitter: JacquesDainat
- Repositories: 2
- Profile: https://github.com/Juke34
Bioinformatician at IRD