GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies

This repository contains source code implementing algorithms used in "GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies", Gritsenko et al. (Bioinformatics, 2012).

The following modules are available:

• Scaffold optimizer (solves the MIQP optimization problem formulation to produce scaffold nucleotide sequences)
• Data linker (uses available information sources to derive scaffolding constraints; currently supports paired ends and mate pairs, and reference genomes)

Additionally the following tools are present:

• Breakpoint counter (assesses scaffold correctness by aligning scaffolds to reference sequences and counting breakpoints)