The Crumble pipeline. The pipeline used after the formation of semi-independent blocks (A). Blocks are aligned (B) and trimmed to remove overlap (C). Overlaps are aligned (D), and the final alignment is formed by concatenation (E). Note that the alignments in (B) and (D) can be performed in parallel.
Roskin et al. BMC Bioinformatics 2011 12:144 doi:10.1186/1471-2105-12-144