Isaac Aligner

The Isaac aligner is designed to align next-generation sequencing data with low-error rates (single or paired-ends). Speed improvements come from the fact that the Isaac aligner has been designed to take full advantage of all the computational power available on a single server node. As a result, the Isaac aligner scales well over a broad range of hardware architectures, and alignment performance improves with hardware capabilities (i.e. clock speed, number of cores, IO bandwidth and memory). Beyond speed and scalability, the Isaac aligner also delivers ease-of-use, flexibility and robustness. The creation of sorted, duplicate-marked BAM files from BCL or FASTQ files is done in a single operation, alleviating the need to rewrite large BAM files multiple times in a typical workflow. Additional command-line options are available to the expert user to finely control the algorithm's inputs, outputs and computational performance.

Accessing the software

To load the module:

$ module load apps/isaac3/

To view a list of command-line options, run the following command:

$ isaac-align --help

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the Isaac aligner website for more information regarding this application.

Last modified: 14 September 2017