PGDSpider version 3.0.0.0 (April 2021)

An automated data conversion tool for connecting population genetics and genomics programs

Introduction

Introduction

PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. It facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances). Besides the conventional population genetics formats, PGDSpider integrates population genomics data formats commonly used to store and handle next-generation sequencing (NGS) data. Currently, PGDSpider is not meant to convert very large NGS files as it loads into memory the whole input file, whose size may exceed available RAM. However, since PGDSpider allows one to convert specific subsets of these NGS files into any other format, one could use this feature to calculate parameters or statistics for specific regions, and thus perform sliding window analysis over large genomic regions.

In the beginning PGDSpider was designed to use a newly developed PGD (Population Genetics Data) format as an intermediate step in the conversion process. PGD is a file format designed to store various kinds of population genetics data, including different data types (e.g. DNA sequences, microsatellites, AFLP or SNPs) and ploidy levels. PGD is based on the XML format and is therefore independent of any particular computer system and extensible for future needs. PGDSpider used PGD to connect population genetics and genomics programs like a spider knits a web. Since version 3.0.0.0 the intermediate PGD file was replaced by an PGD object.

PGDSpider is written in Java and is therefore platform independent. It is user friendly due to its intuitive graphical user interface. PGDSpider allows the user to store his preferred conversion settings for repeated conversions of similar input formats. A command line version of PGDSpider is also provided, making it possible to embed PGDSpider in data analysis pipelines.

System requirements

PGDSpider is written in Java and therefore platform independent, but SUN Java 1.7 RE (or a newer version) has to be installed. Java RE can be downloaded under following link:

http://www.oracle.com/technetwork/java/javase/downloads/index.html

Download and Installation Instructions

1st step:

Install the Java7 RE (or a newer version)

Windows:

• download and install Java RE with following link: http://www.oracle.com/technetwork/java/javase/downloads/index.html

Linux:

• Ubuntu/Debian: Execute the following command as a root user: apt-get install openjdk-8-jre

• Other LINUX distributions: http://www.oracle.com/technetwork/java/javase/downloads/index.html

Mac:

• Apple Computer supplies their own version of Java. Use the Software Update feature (available on the Apple menu) to check that you have the most up-to-date version of Java for your Mac. If you have problems with downloading, installing or using Java on Mac, please contact Apple Computer Technical Support.

2nd step:

Download the PGDSpider application and unzip it on the local drive: PGDSpider (3.0.0.0) - Download

• PGDSpider user manual: PGDSpider manual_v3-0-0-0.pdf

• changes: changelog.txt

• simple example files to do some trial format conversion with PGDSpider: examples.zip

Execute PGDSpider GUI:

• Windows: execute the file PGDSpider3.exe to start the program

• Linux: execute the command ./PGDSpider3.sh to start the program

• Mac and others: execute the command java -Xmx1024m -Xms512m -jar PGDSpider3.jar to start the program

Execute PGDSpider-cli (command line):

• Windows: execute the command PGDSpider3-cli.exe

• Linux: execute the command java -Xmx1024m -Xms512m -jar PGDSpider3-cli.jar

• Mac and others: execute the command java -Xmx1024m -Xms512m -jar PGDSpider3-cli.jar

Formats supported by PGDSpider:

PGDSpider is able to parse 33 and to write 36 different file formats:

Note that, PGDSpider is currently not meant to convert large NGS files as it loads into memory the whole input file, which may lead to memory issues. However, PGDSpider allows one to convert specific subsets of these NGS files into any other format, and this approach can be used to perform sliding windows analyses on large NGS files.

Help

If you have any problems:

• read the user manual: PGDSpider manual_v3-0-0-0.pdf
• read the help file which can be found in the "Config" menu of the PGDSpider

Screenshot

PGDSpider GUI:

SPID Editor:

How to cite PGDSpide and License

Lischer HEL and Excoffier L (2012) PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics 28: 298-299.

Copyright (c) 2007-2021, Heidi E.L. Lischer. All rights reserved.

PGDSpider is distributed under the BSD 3-Clause License. For the full text of the license, see the file LICENSE.txt. By using, modifying or distributing this software you agree to be bound by the terms of this license.

Contact and bug report

If there are any bugs, send me an e-mail. Please give me a short description of the bug and tell me the input and output file format. If it is possible also attach the input file which caused the problem.

PGDSpider is an on-going project. For any comments or suggestions of further file formats, please send me an e-mail.

e-mail: heidi.tschanz-lischer(at)bioinformatics.unibe.ch

Heidi Tschanz-Lischer
Interfaculty Bioinformatics Unit (IBU)
University of Berne
3012 Bern
Switzerland

member of the Swiss Institute of Bioinformatics (SIB)

26.04.2021