SToRM

SToRM is a software tool primarily proposed for mapping SOLiD reads to a reference genome. It was based on seeding techniques adapted to the statistical characteristics of the reads: the default seeds are for example designed (using the Iedera software) to comply with the properties of the SOLiD color encoding, as well as the observed reading error distribution along the read. More information about the seed design and some "ready to use" seed families are available on the framework web page.

SToRM support is currently limited (e.g. it only supports single reads and fixed length reads) : we thus recommend SHRiMP v2 that is much more advanced and with strong support. We however still use SToRM to compare results provided by other read mappers, and thus provide an updated version that now supports color space and also nucleotide space reads (see the compiling option in the Makefile).

The original version of ABI of SToRM was programmed by Marta Gîrdea during the last monthes of her PhD thesis (supervisor Gregory Kucherov). The updated version was proposed by Yoann Dufresne during a short training period, and updated by Laurent Noé (Please contact the last author).

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The program is written in C and was tested on Linux and MacOS platforms (x86 with see/sse2 support, x86-64). Please consult the enclosed README/Makefile file for information about compiling the sources and running the executable.

Related publications

• Noé, L. and Gîrdea, M. and Kucherov, G.: Designing efficient spaced seeds for SOLiD read mapping, Advances in Bioinformatics, Volume 2010, 2010
• Noé, L. and Gîrdea, M. and Kucherov, G.: Seed design framework for mapping SOLiD reads, In Proceedings of RECOMB 2010, Lisbon, August 12 – 15, 2010
• Gîrdea, M. and Noé, L. and Kucherov, G.: Read mapping tool for AB SOLiD data, WABI 2009, Philadelphia, September 12 – 13, 2009