SPAligner is a standalone tool for aligning long diverged molecular (both nucleotide and amino acid) sequences against assembly graphs produced by the popular short-read assemblers. The project stemmed from our previous efforts on the long-read alignment within SPAdes (hybridSPAdes) assembler. A more detailed description can be found in our biorXiv preprint.


SPAligner is implemented on top of SPAdes and will be available soon as a part of SPAdes package. For now, one can download, build, and try a pre-release version of SPAdes package including SPAligner.
For more instructions on SPAligner usage please go to src/projects/spaligner/ in downloaded zip archive.

Also see the main SPAdes page for system requirements and build instructions.


In case of any questions, suggestions, bug reports, please write to  or directly to Tatiana Dvorkina.