Dear all

The MetaPhlAn2 use bowtie2 to align metagenomics reads to clade specific marker genes so that the speed is very fast. However, we do not know whether the very sensitive option for bowtie2 is too stringent or not. When using bowtie2 to map metagenomics reads to genes, whether it is possible to get an identity value or e-value for each mapped reads. The bowtie2 indeed have some parameters for alignment like gap penalty, gap extending and mismatch, but there is no way to evaluate the alignment quality for every mapped reads. Thanks