/// <summary>
/// Assemble the list of sequence reads
/// </summary>
/// <param name="inputSequences">List of input sequences</param>
/// <returns>Assembled output</returns>
public IDeNovoAssembly Assemble(IList <ISequence> inputSequences)
{
ValidateAllSequences(inputSequences);
// Remove ambiguous reads and set up fields for assembler process
Initialize(inputSequences);
// Step 1, 2: Create k-mers from reads and build de bruijn graph
CreateGraph();
// Estimate and set default value for erosion and coverage thresholds
EstimateDefaultThresholds();
// Step 3: Remove dangling links from graph
UnDangleGraph();
// Step 4: Remove redundant paths from graph
RemoveRedundancy();
// Perform dangling link purger step once more.
// This is done to remove any links created by redundant paths purger.
UnDangleGraph();
// Step 5: Build Contigs
IList <ISequence> contigSequences = BuildContigs();
PaDeNAAssembly result = new PaDeNAAssembly();
result.AddContigs(contigSequences);
_graph.Dispose();
return(result);
}
/// <summary>
/// Assemble the list of sequence reads. Also performs the
/// scaffold building step as part of assembly process.
/// </summary>
/// <param name="inputSequences">List of input sequences</param>
/// <param name="includeScaffolds">Boolean indicating whether scaffold building step has to be run</param>
/// <returns>Assembled output</returns>
public IDeNovoAssembly Assemble(IList <ISequence> inputSequences, bool includeScaffolds)
{
PaDeNAAssembly assemblyResult = (PaDeNAAssembly)Assemble(inputSequences);
if (includeScaffolds)
{
// Step 6: Build _scaffolds
IList <ISequence> scaffolds = BuildScaffolds(assemblyResult.ContigSequences);
if (scaffolds != null)
{
assemblyResult.AddScaffolds(scaffolds);
}
}
return(assemblyResult);
}
