Align shotgun metagenomics to reference protein database

Question

[zhangdengwei]

Hi all,

I would like to align the shotgun metagenomics data to a set of protein sequences of interest to estimate their abundance in the metagenome. I found [paladin][1] can accomplish this task, which is on the basis of bwa algorithm. However, I found the alignments sometimes are greedy, with some mismatches or insertions present. There are no parameters to control those mismatches. I wonder how to control the number of mismatches and indels in the alignment. Is there any alternative for this task?

Any suggestion would be greatly appreciated.