Isaac aligner version 4
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* SAAC-1347 Default max read length to allow for 600
* SAAC-1346 Overestimation of splits in a bin due to large coverage spikes
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Isaac Genome Alignment Software Copyright (c) 2010-2017 Illumina, Inc. All rights reserved.

This software is provided under the terms and conditions of the GNU GENERAL PUBLIC LICENSE Version 3

You should have received a copy of the GNU GENERAL PUBLIC LICENSE Version 3 along with this program. If not, see

Isaac aligner

To configure and install the product, see the src/INSTALL.

The component algorithms for the Isaac aligner are intended for developers to re-use and improve them. This version is not commercially supported and provided as is under GNU GENERAL PUBLIC LICENSE Version 3. Isaac is included in the HiSeq Analysis Software described here which is commercially supported, and in the Isaac apps on the BaseSpace platform. For more information, see our blog post.

See src/Changes for the release history details.

Quick start guide

The following example command will get you through aligning some example PhiX data. For more examples and details please see src/markdown/

Process fastq data

Analyze a pair of fastq files and produce bam output.

$ <isaac>/bin/isaac-align -r <isaac>/share/*/data/examples/PhiX/iGenomes/PhiX/NCBI/1993-04-28/Sequence/Chromosomes/phix.fa -b <isaac>/share/*/data/examples/PhiX/Fastq -f fastq --use-bases-mask y150,y150 -m40