fgbio

fgbio is a command line toolkit for working with genomic and particularly next generation sequencing data.

See the latest available tools here.

Quick Installation

The conda package manager (configured with bioconda channels) can be used to quickly install fgbio:

conda install fgbio

To install fgbio without extra dependencies (e.g. R), use the command:

conda install fgbio-minimal

Using the Project Jar File Directly

Releases of fgbio are available from the GitHub Releases page for the project. Start by downloading the .jar file for the latest release.

To run fgbio you will need Java 8 (aka Java 1.8) or later installed. To see the version of Java currently installed run the following in a terminal:

java -version

If the reported version on the first line starts with 1.8 or higher, you are all set.

Once you have Java installed and a release downloaded you can run:

• Run java -jar fgbio-2.3.0.jar to get a list of available tools
• Run java -jar fgbio-2.3.0.jar <Tool Name> to see detailed usage instructions on any tool

When running tools we recommend the following set of Java options as a starting point though individual tools may need more or less memory depending on the input data:

java -Xmx4g -XX:+AggressiveOpts -XX:+AggressiveHeap -jar fgbio.jar ...

To save typing this every time you may wish to setup a shell alias, for example:

alias fgbio="java -Xmx4g -XX:+AggressiveOpts -XX:+AggressiveHeap -jar /path/to/fgbio.jar

Documentation

Each tool has detailed usage and argument documentation that can be viewed at the command line by running the tool in question with no arguments.

Documentation is also available online:

• Tool usage documentation is available here
• Documentation of the various metrics files is available here
• API documentation for developers is available through javadoc.io.
• Web utility for validating Read Structures is available here
• Web utility for validating a Sample Sheet for DemuxFastqs is available here

Getting Help

The primary mechanism for getting help is to log an issue on the project’s GitHub Issues page.

Before Logging An Issue

• Make sure you are running the latest release of fgbio
• Search both open and closed issues for similar problems
• Ensure that your input files are valid (for BAM files we kindly request you run Picard’s ValidateSamFile before logging issues)

When Logging An Issue

If requesting help with a tool that is failing or producing undesirable results, please include:

• The full command line used to invoke the tool
• The terminal output produced by the tool while running
• Information on the operating system you are running, using uname -a
• Information on the version of Java you are running, using java -version

License

fgbio is open source software released under the MIT License.