This plug-in allows the user to map and align short reads against a reference sequence with sequencer-specific algorithms including correction of G/C bias in Illumina, homopolymer error in Ion Torrent and 454, and color error in SOLiD data.
All Omixon plug-ins are designed to work with the other high-throughput sequencing tools within the CLC Genomics Workbench.
The Omixon plugin was originally called the 'Gapped SOLiD Alignment plugin', this name has been changed now that the plug-in also supports data from other sequencers.
The Omixon PreciseAlign plugin is based on the Omixon Letter Space and Omixon Color Space Toolkits. It performs both rough read mapping and fine statistical alignment steps. Variants are reported with statistical confidence measures that take into account alignment accuracy and sequence quality scores. The output from the plug-in is a standard CLC bio read-mapping object (or table of objects), which can be analysed using the CLC bio SNP Detection and DIP Detection tools (generating reports and/or reference annotations), or exported from the Workbench as a SAM file for further analysis.
Note that the Omixon PreciseAlign plug-in can be used in place of the CLC Bio 'Map Reads To Reference' tool in complex workflows such as Targeted resequencing, if the input is SOLiD, Ion Torrent, Illumina or Roche 454 short reads.
This version of the Omixon plugin was developed against version 5.0 of the CLC Genomics Workbench. It has not been tested with earlier versions.
The basic work flow supported by the CLC Genomics Workbench and the Omixon PreciseAlign plug-in is this:
- Import or download reference genome (import the file from clcbio.com into the CLC Genomics Workbench to get started with e.g. the human genome)
- Import sequencing data (using the High-throughput Sequencing Data import)
- Perform read mapping using the Omixon PreciseAlign plug-in
- Run SNP and DIP detection to detect variants in the sequencing data
Check the user manual of the CLC Genomics Workbench for more info on steps 1, 2 and 4. Check the user manual of the Omixon PreciseAlign plug-in for more info on step 3, and more background info on the algorithms being used.