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HiLive Manual

Content:

• HiLive overview
• License
• [Requirements] and setup
• [Basic] usage
• [Advanced] usage and parameter details

HiLive overview

HiLive is a general read mapping tool that maps Illumina HiSeq (or comparable) reads right in the moment when they are produced. The read mapping process starts already when the sequencer is running, as soon as the first basecalls for each read are writen out by the machine. Therefore, HiLive effectively uses the time to map the first parts of the reads when the sequencer is still running. This means, read mapping is finished as soon as the sequencer is finished, circumventing typical steps like FastQ file generation and conventional read mapping.

HiLive is built for high performance applications where time and throughput are the most critical factors. For example, HiLive can significantly reduce processing time in diagnostics applications such as whole exome sequencing or gut microbiome analyses. Also sequencing facilities can potentially reduce sample processing time to deliver results faster. Unfortunately, HiLive is not a "desktop" application and requires good hardware infrastructure to release its full potential.

License

HiLive is Open Source software and free to use:

Copyright (c) 2015, Martin S. Lindner.
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Project Members:

• Martin S. Lindner (admin)