#117 comparative assembly feature

[Anonymous]

Comparative assembly using synteny of related genomes can provide a more efficient scaffolding of de novo assemblies. CA should have a feature that compares contigs from 5-consensus to a reference fasta file. The sensitivity of the alignment algorithm should be BLASTN like (wordsize 11 for non closely related species). The contig order proposed by comparison with the reference should support the cgw step, but mate pair information should have a higher priority.