piquant is a pipeline of Python scripts to help assess the accuracy of quantification of transcripts from RNA-sequencing data. It has three stages:

• Simulation: RNA-seq reads are simulated from a starting set of transcripts with known abundances, under specified combinations of RNA-sequencing parameters.
• Quantification: A number of transcriptome quantification tools estimate transcript abundances for each set of simulated reads.
• Analysis: The comparative accuracy of expression estimates calculated by each tool can be assessed via a range of automatically generated statistics and graphs.

The latest piquant documentation can be found here.

Note: as piquant has a number of dependencies on other Python packages, it is strongly recommended to install in an isolated environment using the virtualenv tool. The virtualenvwrapper tool makes managing multiple virtual environments easier.

After setting up virtualenv and virtualenvwrapper, create and work in a virtual environment for piquant using the virtualenvwrapper tool:

mkproject piquant

Clone the piquant GitHub repository into this environment:

git clone https://github.com/lweasel/piquant.git .

Install the piquant package and scripts, and their Python package dependencies, into the virtual environment by running:

pip install .

in the tool's top-level directory. Note that it may take some time to install and build the dependencies.

Run unit tests for piquant using the command:

py.test test

in the tool's top-level directory.

• 1.1 (27/03/15):
  • Added gene-level analysis
  • Added strandedness and transcript "noise" as sequencing parameters
  • Added quantification tool time and memory resource usage plots
  • Separate parent directories for read and quantification directories
  • Some hardcoded quantification and analysis values made user-definable
• 1.0 (28/10/14): First full release
• 0.1: Initial beta development