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  • MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to...

MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s)

https://github.com/marbl/MashMap

MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It does not compute the alignments explicitly, but rather estimates a k-mer based Jaccard similarity using a combination of Winnowing and MinHash. This is then converted to an estimate of sequence identity using the Mash distance. An appropriate k-mer sampling rate is automatically determined given minimum local alignment length and identity thresholds. The efficiency of the algorithm improves as both of these thresholds are increased.