Read Processing and Reactivity Generation for SHAPE-Seq

Spats processes reads and calculates SHAPE reactivities for SHAPE-Seq experiments on multiple RNAs. It accepts raw paired-end sequencing reads in fastq format, and a target sequence file containing the sequences of RNAs present in the experimental pool. Spats then performs read alignment to calculate distributions of read ends in the SHAPE (+) and (-) channel for each nucleotide in each RNA. Spats then estimates nucleotide resolution SHAPE reactivities for each RNA, using a model-driven maximum likelihood procedure based on a model of the reverse transcriptase process used in the SHAPE-Seq experiment. Spats is a collaborative effort between the Aviran Lab at UC Davis, the Pachter Lab at UC Berkeley, the Trapnell Lab at the University of Washington, and the Lucks Lab at Northwestern University.

Spats is provided under the OSI-approved Boost License.
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Related Tools

  • Bowtie: Ultrafast short read alignment
  • FastX Toolkit: FASTQ/A short-reads pre-processing tools


Other Contributors


1.0.2 release - 5/30/17

Spats v 1.0.2 is now available for download. This release allows us to create and distribute binaries for Linux and Mac with Boost precompiled. Is still dependent on bowtie v0.12.8 and cutadapt being in the user's path.

1.0.1 release - 9/10/16

Spats v 1.0.1 is now available for download. This release fixes a bug in spats for proper option parsing of number of mismatches allowed. Additionally, we included an optional utility to split the output reactivities file from spats into individual files per target sequence.

As part of this release, Spats is now officially hosted on GitHub at

1.0.0 release - 3/31/16

Spats v 1.0.0 is now available for download. This release mostly focuses on moving away from the fastxtoolkit which has been mostly replaced with cutadapt in the adapter_trimmer. Cutadapt allows for more flexibility including the ability to include mismatches in the adapter trimming step so that spats can handle mismatches downstream. There are also several more options available for adapter trimming, see the manual for more information. In addition, there is also test code for correct read mapping in the test/ directory.

This release sets up the eventual deprecation of using the fastx tools. Note: only fastx_revcomp is still used by spats with this release.

As part of this release, spats is now officially hosted on GitHub at

New SHAPE-Seq Experiment Simulator - 5/24/2015

A SHAPE-Seq simulator is now available for download as a Matlab package from The code allows one to simulate SHAPE-Seq experiments under varying conditions and to emulate the resulting sequencing data, as part of the experiment design process. The software includes an implementation of SHAPE-Seq’s maximum-likelihood reactivity estimation pipeline to process the generated data. Details about this in silico framework can be found in Aviran and Pachter (2014) and in

0.8.0 release - 9/4/2014

Spats v 0.8.0 is now available for download. This release was made to support SHAPE-Seq v2.0, an experimental upgrade to the SHAPE-Seq experimental workflow that removes the need to use internal RT primer sites or additional flanking RNA sequences to act as RT priming sites. SHAPE-Seq 2.0 ligates a linker after RNA modification, which is then used to prime the RT reaction. Details about SHAPE-Seq 2.0 can be found in Loughrey, Watters et. al. (2014).

The major difference between v0.7.0 and v0.8.0 is an updated adapter trimming algorithm. This now requires installation of a modified fastx toolkit (fastx_spats_toolkit v0.1.0) which can be found here here. A new python script was made to implement the trimming algorithm, which should be used as a pre-process step before calling spats. Details of how to use the new implementation can be found in the manual.

We have also greatly expanded the installation instructions.

A special thanks of Gordon Assaf for assisting with the coding and release of fastx_spats_toolkit_v0.1.0 .

This software is a work in progress - it is a beta release, and new features will continue to be added over time. To suggest a feature, report a bug, or report a website error please email us

0.7.0 release - 4/10/2012

The first public release of Spats is now available for download. Spats is a program for the analysis of sequencing information to determine SHAPE reactivities in a SHAPE-Seq experiment. It runs on Linux and OS X.

Spats takes as input files containing paired-end reads in fastq format, a file containing the sequences of RNA molecules contained in the experimental pool in FASTA format, and reports reactivities for each nucleotide of each RNA in a flat file format.

This software is a work in progress - it is a beta release, and new features will continue to be added over time. To suggest a feature or report a bug, please email us