pufferfish | efficient index for the colored , compacted , de Bruijn graph | Genomics library

pufferfish is a C library typically used in Artificial Intelligence, Genomics applications. pufferfish has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

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. It supports aligning to transcriptome as well as genome, but currently supports only contiguous alignments (i.e. spliced-alignment is not yet implemented). However, the design means that one can use Puffalign to align reads to a collection of genomes (or/and transcriptomes), as well as to a joint index that contains both the genome and the spliced transcripts. Another feature of the aligner is introducing a list of decoys along with the main sequences to the index. A read is discarded if it aligns better to a decoy sequence rather than a sequence in the main list. One of the usecases of such feature is in improving the transcript alignment accuracy in case of retained introns, processed pseudogenes, etc..