GeneRic ASembly Scaffolder
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Common
breakpointCounter
coverageUtil
dataFilter
dataLinker
dataSelector
dataSimulator
kmer
manual
readCleaner
readDiff
scaffoldOptimizer
LICENSE Adding LICENSE text file. Jan 16, 2012
Makefile
Makefile.config
README.md

README.md

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)