sparse vs. dense index

[rob-p]

Q: When indexing a reference (splici or otherwise), salmon provides the option to produce a sparse index (by providing the --sparse flag to the index command) or a dense index (the default). Should I use the sparse index or the dense index?

[rob-p]

A: Both indices should produce identical mapping results. Therefore, the choice of which to use depends on the resource constraints in the environment where you will be processing your data. The sparse index is available to allow the user to make a tradeoff of time versus memory during quantification. In general, mapping reads against the the dense index index can be ~20% faster than against the sparse index (with the biggest difference appearing in --sketch mode), but can use 30-40% more RAM during mapping. If, during mapping, memory is at a premium, you may wish to use the sparse index. On the other hand, if extra memory is available for the relevant processes where your mapping is being performed, the dense index will get your results a bit more quickly.