Genomic Software - Gapped SOLiD alignment analysis

The Omixon Gapped SOLiD Alignment plug-ins contain sequencer specific, highly accurate algorithms for reference based mapping, alignment and analysis. The Gapped SOLiD Alignment server and workbench plug-ins are intended for the analysis of color space data produced by Life Technologies SOLiD sequencers. Omixon plug-ins are designed to work with other high-throughput sequencing tools within the CLC Genomics Workbench.

Omixon offers a Gapped SOLiD Alignment plug-in for the CLC Bio Genomics Workbench and for the CLC Bio Genomics Server. The plug-ins provide Omixon's accurate SOLiD short read mapping and alignment expertise via the CLC bio platform.

User benefits
• Highest possible accuracy for short read NGS analysis.
• The lowest amount of unmapped or incorrectly mapped reads. Less wasted sequences and wasted consumables.
• Find more variants than your competitors from the same run.
• Automatic handling of lower quality bases without dismissing entire short reads or trimming.
• No need to run pre-filtering tools. Automatic re-calibration of quality scores is part of the alignment.
• No need to run post-alignment tools such as variant equivalents since these are automatically handled at alignment level.
• No need to learn a range of parameters. Most parameterization is handled automatically. The user needs to select sensitivity, maximum mismatches and gaps.
• High performance: save on computing resources since this analysis is faster than the Smith-Waterman based short read aligners.

Gapped SOLiD Alignment
The Omixon Gapped SOLiD Alignment plug-in is based on the Omixon Color Space Toolkit and the algorithms described in Csuros, Juhos, Berces "Fast Mapping and Precise Alignment of AB SOLiD Color Reads to Reference DNA" Springer Lecture Notes in Bioinformatics 6293:176-188, 2010. It was designed to analyze short read sequencing data obtained from Life Technologies SOLiD next generation sequencing (NGS) instruments.

In contrast to other short read mapping and alignment tools the Omixon algorithms were designed specifically for a particular sequencer, in this case the Life Technologies SOLiD sequencer and its data error model. The mapping uses a spaced seed technique with greedy extension to find the most likely location of the short reads on the reference. In such an alignment, reads are mapped to approximate genome positions, allowing for a pre-specified bound on sequence divergence that combines nucleotide mismatches, gaps, and sequencing errors. The precise alignment relies on a pair hidden Markov model framework, combining DNA sequence evolution models and sequencing errors (from read quality values).

The Omixon Gapped SOLiD Alignment plug-ins provide the highest accuracy and gives you the best chance to find the diagnostically or biologically important variant you are looking for. This CLC Genomics plug-ins are designed to work with the other High-throughput sequencing tools and plug-ins provided by the Workbench. You can use the SNP and DIP (indel) detection tools of the workbench to call variants from the aligned reads.

Precise Variant Detection
The comprehensive probabilistic model incorporates quality scores from the sequencer, and a DNA mutation model (including G/C content, transitions/transversions, and sequence divergence). This allows for statistical confidence measures with no ad-hoc alignment scoring or thresholds.

Software Link: Genomic Software - Gapped SOLiD alignment analysis

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