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pufferfish website  

Puffaligner is a fast, sensitive and accurate aligner built on top of the Pufferfish index. It tries to occupy a less-well-explored position in the space of read aligners, typically using more memory than BWT-based approaches (unless there are highly repetitive references), but considerably less than very fast but memory-hungry aligners like STAR. Puffaligner is based on hashing relatively long seeds and then extending them to MEMs, and so it is very fast (typically much faster than approaches based on arbitrary pattern matching in the BWT). It takes a seed -> chain -> align approach similar to BWA-MEM and minimap2.

Environment Modules

Run module spider pufferfish to find out what environment modules are available for this application.

System Variables

  • HPC_PUFFERFISH_DIR - installation directory
  • HPC_PUFFERFISH_BIN - executable directory
  • HPC_PUFFERFISH_IMAGE - apptainer image