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.


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 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 .