tud-scaffolding

GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies This SVN 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) News This repository has been moved to GitHub

LICENSE
Makefile
Makefile.config
breakpointCounter
breakpoint.cpp
Configuration.cpp
BreakpointCount.h
Configuration.h
Defines.h
Makefile
BreakpointCount.cpp
Common
Aligner.cpp
AlignmentReader.cpp
Converter.cpp
DataStore.cpp
DataStoreReader.cpp
DataStoreWriter.cpp
Helpers.cpp
MummerCoordReader.cpp
MummerTilingReader.cpp
ReadCoverage.cpp
ReadCoverageReader.cpp
ReadCoverageRepeatDetecter.cpp
ReadCoverageWriter.cpp
Reader.cpp
Sequence.cpp
Timers.cpp
Writer.cpp
XATag.cpp
AlignerConfiguration.h
Aligner.h
AlignmentReader.h
Converter.h
DataStore.h
DataStoreReader.h
DataStoreWriter.h
Globals.h
Helpers.h
MinMax.h
MummerCoord.h
MummerCoordReader.h
MummerTiling.h
MummerTilingReader.h
ReadCoverage.h
ReadCoverageReader.h
ReadCoverageRepeatDetecter.h
ReadCoverageWriter.h
Reader.h
Sequence.h
Timers.h
Writer.h
XATag.h
Makefile
AlignerConfiguration.cpp
coverageUtil
coverage.cpp
Configuration.h
Defines.h
Makefile
Configuration.cpp
dataFilter
ContigInfo.cpp
filter.cpp
Configuration.h
ContigInfo.h
Defines.h
Makefile
Configuration.cpp
dataLinker
linker.cpp
PairedReadConverter.cpp
SequenceConverter.cpp
Configuration.h
Defines.h
PairedReadConverter.h
SequenceConverter.h
Makefile
Configuration.cpp
dataSelector
selector.cpp
Configuration.h
Defines.h
Makefile
Configuration.cpp
dataSimulator
ContigInformation.cpp
simulator.cpp
Configuration.h
ContigInformation.h
Defines.h
Makefile
Configuration.cpp
kmer
kmer.cpp
Location.cpp
Configuration.h
Defines.h
Location.h
Makefile
Configuration.cpp
readCleaner
Configuration.cpp
PairedReadProcessor.cpp
Configuration.h
Defines.h
PairedReadProcessor.h
Makefile
cleaner.cpp
readDiff
diff.cpp
Configuration.h
Defines.h
Makefile
Configuration.cpp
scaffoldOptimizer
Configuration.cpp
ContigOverlapper.cpp
DPGraph.cpp
DPSolver.cpp
EMSolver.cpp
ExtendedFixedMIQPSolver.cpp
FixedMIQPSolver.cpp
GAIndividual.cpp
GAMatrix.cpp
GASolver.cpp
GraphViz.cpp
IterativeSolver.cpp
MIQPSolver.cpp
NWAligner.cpp
optimizer.cpp
OverlapperConfiguration.cpp
RandomizedGreedyInitializer.cpp
RelaxedFixedMIQPSolver.cpp
ScaffoldComparer.cpp
ScaffoldConverter.cpp
ScaffoldExtractor.cpp
SolverConfiguration.cpp
BranchAndBound.h
Configuration.h
ContigOverlapper.h
Defines.h
DPGraph.h
DPSolver.h
EMSolver.h
ExtendedFixedMIQPSolver.h
FixedMIQPSolver.h
GAIndividual.h
GAMatrix.h
GASolver.h
GraphViz.h
IterativeSolver.h
MIQPSolver.h
NWAligner.h
OverlapperConfiguration.h
RandomizedGreedyInitializer.h
RelaxedFixedMIQPSolver.h
ScaffoldComparer.h
ScaffoldConverter.h
ScaffoldExtractor.h
SolverConfiguration.h
Solver.h
Makefile
BranchAndBound.cpp
manual
manual.tex
Makefile