CLASS2

CLASS2 - transcript assembly from RNA-seq sequences

CLASS2 is a fast and accurate program for transcript assembly of RNA-seq reads aligned to a reference genome. CLASS2 uses the splice graph model to represent a gene and its splice variants, and a dynamic programming optimization algorithm to score and select a subset of transcripts most likely present in the sample. CLASS2 aims to capture as much alternative splicing variation as possible with very high accuracy.

CLASS2 is described in:

• Song, L., S. Sabunciyan and L. Florea (2016). CLASS2: Accurate and Efficient Splice Variant Annotation from RNA-seq Reads, Nucl. Acids Res. 44(10):e98. [Medline]

Download CLASS2 here. Simulated reads and alignments from the manuscript can be accessed here.

Download and installation procedure

The program was written for Linux platforms and may require some modifications to run on a different Unix platform.

To install and run CLASS2, you will need to download and install the samtools package for managing large short read alignment files.

1. Download and install the samtools package, if not already on the system. Save the executables somewhere in your PATH.

2. Download and unpack the gzipped tar file CLASS.tar.gz

           gunzip < CLASS.tar.gz | tar -xvf -
   

3. The tar will unpack into a directory named CLASS.[version]. (You'll see what the precise name is while tar is unpacking.) Make that directory current.

           cd CLASS.*
   

4. Follow the instructions in the COMPILING file, included, to compile.

Versions

Current version is 2.1.3.

This work was supported in part by NSF awards ABI-1356078 and IOS-1339134 to Liliana Florea.