Salmon v0.5.0

This release of Salmon brings some significant new features (hence the move from v0.4.X to v0.5). Note: The update to the indexing infrastructure means that you will have to re-build any existing indices (even if you choose to use the original FMD-based index), since the index version has changed and extra information is now recorded in the indices.

New Features

• Bootstrap estimates — You can now generate bootstrap samples to measure (technical) variance in the abundance estimates. This behavior is enabled by passing --numBootstraps k to the quant command. This will generate k bootstrap samples and place them in a file quant_bootstraps.sf. Bootstrap sampling is parallelized using the same number of threads requested for quantification, and though generating bootstraps does increase overall runtime, the process is very efficient. In addition to being generally useful for assessing confidence in the abundance estimates, these bootstraps allow Salmon to be used with a new class of differential expression tools.
• (Optional) Quasi-mapping based index — Salmon now supports two different types of indices. The FMD index, which is the index that Salmon has traditionally used up until this release, and a new suffix-array-based quasi-mapping index. When building the index, you now must specify what type of index you wish to build. The type of index is specified with the --type argument, and the options are --type fmd (the original index) or --type quasi (the new index). Support for both types of indices is being maintained in this release because the quasi-index is still mildly experimental (though seems to work very well in practice). You need only specify this option when building the index. Salmon will automatically determine how quantification should proceed based on the type of index with which it is run. The main benefit of the new quasi index type is that it speeds up mapping, sometimes significantly.