Bioinformatics analysis Software - Omixon Letter Space Toolkit

The Omixon Letter Space Toolkit is a suite of tools for performing bioinformatics analysis. The main tool is a gapped read mapper and alignment tool called ORM. The toolkit also contains a number of utilities for reformatting, sorting, filtering and parsing bioinformatics data, and handling very large files across a number of platforms.

The current version of Omixon Letter Space Toolkit is the first commercial version. A request for an evaluation downloaded can be made directly from this page.

The Toolkit allows mapping of reads from the Illumina, Roche 454 and Ion Torrent platforms. In theory, it should also be able to map letter space reads from the Life Technologies 5500 platform.

Note that we have two toolkits, there is also an Omixon Color Space Toolkit, which is for mapping and aligning color space data produced by Life Technologies series 4 (SOLiD) sequencers.

Command line Letter Space Toolkit
The main tools of the Omixon Letter Space Toolkit are available as a standalone Java application, which can be run from the command line. These tools automate the analysis, as well as automatically run it in parallel (if multiple processors are available).

The command line Toolkit comes with some supporting scripts, plus a comprehensive readme file that describes how to run the tools. An evaluation version of The Letter Space toolkit can be downloaded and tried for free.

Letter Space Toolkit features
The Toolkit includes highly accurate tools for detecting micro indels, SNPs and MNPs.

It offers a solution to map letter reads with a moderate distance (up to 30% sequence divergence) from reference genomes. It poses no restrictions on the size of the reference, which, combined with its high sensitivity, makes the Letter Space Toolkit well-suited for targetted sequencing projects and diagnostics.

The ORM tool within the Letter Space Toolkit is also extremely fast, and offers 'variable density indexing', where regions of greater interest (such as the exome) can be indexed more densely to improve sensitivity in those areas.

User Benefits
• Mapping of reads from the Illumina, Roche 454 and Ion Torrent platforms
• Finds larger indels than any other tool
• Performance is linear in respect to edit distance
• Very simple to run
• Choice of pre-set 'profiles' for species, platform and speed

Innovative Alignment
The Letter Space Toolkit contains sequencer-specific algorithms, settings and error correction models.

The main module of the Letter Space Toolkit - called ORM - follows the seed-and-extend paradigm. Letter space (base space) reads are indexed by ORM using spaced seeds and approximately mapped to a reference sequence database. ORM uses a second, much smaller seed to help to filter the approximate mappings. The underlying data structures are extremely economical for memory use, yet still provide high flexibility for trade-offs between sensitivity and specificity.

The fine alignment uses a combination of information and algorithms to produce its results, including the quality scores from the sequencer and a DNA mutation model. There are two main alignment techniques, a 'bridging' technique for smaller reads (such as Illumina short reads) where only one indel is expected, and a 'lacing' technique which allows for more indels per read, to cater for the longer Ion Torrent and Roche 454 reads.

Software Link:  Bioinformatics analysis Software - Omixon Letter Space Toolkit

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