gsnap vs bbmap

Question

[Ada]

My gsnap alignment scores were much lower (77% vs 95%) than scores received from BBMAP. How can I go about rectifying this problem?

[lieven.sterck]

you mean as in amount of reads aligned?

First thing to check is that they are using the same parameter settings (or at least roughly). But also keep in mind that there will always be differences between different tools.