Spats v1.0.2

Reorginzation of build process, simpler/easier source builds. Includes precompiled binaries for Linux/Mac.

Spats v1.0.1

Spats v1.0.1 is a minor update to the Spats pipeline. This updates includes:

• A bugfix to spats to allow proper parsing of arguments. Previous versions unintentionally set the -m and --num-mismatches options to the same values. This has been fixed.
• Inclusion of a new utility called reactivities_split, which parses spats reactivities.out into individual files for each target.

Spats v1.0.0

Spats v1.0.0 is an update to the Spats pipeline for processing Next-Generation Sequencing Reads as part of SHAPE-Seq experiments. The major difference between v0.8.0 and v1.0.0 is the migration to the cutadapt utility for removing adapter sequences from the fastxtoolkit. This release still relies on fastx_revcomp, but the code is structured to completely move away from fastxtoolkit in the future.

We have also migrated all hosting of spats to github. Online documentation can now be found at the spats github page: http://luckslab.github.io/spats/index.html which includes links to an installation guide and usage manual.

Spats v0.8.0

Spats v0.8.0 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, Settle, Lucks (2014) "SHAPE-Seq 2.0: Systematic Optimization and Extension of High-Throughput Chemical Probing of RNA Structure with Next Generation Sequencing".

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.

A new python script apdater_trimmer.py 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 at the spats 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 at spats dot shape at gmail dot com .