Isaac Genome Alignment Software Copyright (c) 2010-2014 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 https://github.com/illumina/licenses/.

#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 commands will get you through preparing the reference and aligning some example PhiX data. For more examples and details please see src/markdown/manual.md

##Prepare reference genome

This step can take long time on bigger genomes. Normally it is done once per reference and the output is reused in further data analyses.

$ <isaac>/bin/isaac-sort-reference -g <isaac>/data/share/*/data/examples/PhiX/iGenomes/PhiX/NCBI/1993-04-28/Sequence/Chromosomes/phix.fa -o ./PhiX

##Process fastq data

Analyse a pair of fastq files and produce bam output.

$ <isaac>/bin/isaac-align -r ./PhiX/sorted-reference.xml -b <isaac>/data/share/*/data/examples/PhiX/Fastq -f fastq --use-bases-mask y150,y150 --variable-read-length yes -m10