Bioinformatics Example Repository

This repository contains example tools and pipelines discussed on my blog.

Posts

Here are some posts you may be interested in:

• Sample Demultiplexing an Illumina Sequencing Run
• Single Strand UMI Somatic Variant Calling

Getting Started

To run bfx-examples 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 bfx-examples-tool.jar to get a list of available tools
• Run java -jar bfx-examples-pipelines.jar to get a list of available pipelines
• Run java -jar bfx-examples-tool.jar <Tool Name> to see detailed usage instructions on any tool (similarly for pipelines)

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 bfx-examples-tools.jar ...

Documentation

Each tool and pipeline 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
• Pipeline usage documentation is available here
• Documentation of the various metrics files is available here