What is SToRM ?

SToRM is a software tool primarily proposed for mapping Illumina or SOLiD reads to a reference genome. It is based on seeding techniques adapted to the statistical characteristics of the reads: the seeds are designed (using the Iedera software) to comply with the properties of the Illumina base encoding, or the SOLiD color encoding, and the observed reading error distribution.

More information and examples can be found,

Note first that SToRM supports equal-length reads, and does not provide mate-pair/paired-end support by now. We otherwise recommend SHRiMP v2.

Note also that you can run SToRM in successive steps to gain both in sensitivity and speed. Indeed, it is possible to output unmapped reads from a given step as a new FASTQ file, for further and more refined analysis (smaller seeds or any better parameters choice). An example is given in the README file.

The original version of ABI of SToRM was programmed by Marta Gîrdea during the last monthes of her PhD thesis (main supervisor Gregory Kucherov). The updated version was proposed by Yoann Dufresne during a short training period, and updated by Laurent Noé (with strong testing from Karel BÅ™inda).



(last updated version)

Last update: January 3, 2016

storm-binaries-0.0099: osx_x64, linux_x64

(last binaries version)

Last update: November 25, 2014


(last sources for binaries version)

Last update: October 15, 2014


(original version of ABI paper)

Last update: June 11, 2010

The program is written in C and was tested on Linux and MacOS platforms (x86{-64} with sse/sse2/avx2/avx512bw support). Please consult the enclosed README file for information about compiling the sources and running the executables.