Can Maq align reads longer than 32bp?
Yes. The maximum allowed read length is 63bp. I can loose the limit at the cost of speed and memory usage. • Can I use Maq to align 454 reads or capillary reads? No. For the moment, Maq can only map reads at most 63bp in length. Capillary reads and 454 reads are much longer than that. In addition, Maq usually performs ungapped alignment whereas capillary and 454 reads usually contain many short indels. • Can I use Maq to find short indels? Yes, but only if you have paired end reads. Maq has a module to find break points with single end reads, but it does not work well in all cases. This module is not accurate and not ready for end users. • Is Maq able to deal with reads with variable lengths? No and yes. In alignment, all the reads must be in the same length. However, you can `mapmerge’ several alignments from reads in different lengths and after that all the subsequent maq commands accept variable lengths.
