Is there a suggested mapper and variant caller for mapping a consensus sequence (contigs) to a reference? Or is there a suggested method for doing this with mappers that don't support it. Currently we've been trying to use bowtie2 and have shredded contigs (with overlapping segments and 5x coverage) map with a reference, but the results are way too different from the results of mapping the reads against the reference.
Any thoughts?
Any thoughts?