Iteratively, we replace the reference with the consensus and try to align the reads, for which we could not find any acceptable alignment previously. Our experiments on a dataset consisting of approximately 31,000 454 pyrosequencing reads generated from a 5.2kb-long HCV fragment (see data description in Results and Discussions) show that 85% of reads are uniquely aligned onto the reference sequence and an additional 9% of the reads are aligned onto the final consensus sequence. Reads that cannot be aligned onto the final consensus are removed from the further consideration. 