GenMap: ultra-fast computation of genome mappability.

ABSTRACT:

Motivation

Computing the uniqueness of k-mers for each position of a genome while allowing for up to e mismatches is computationally challenging. However, it is crucial for many biological applications such as the design of guide RNA for CRISPR experiments. More formally, the uniqueness or (k, e)-mappability can be described for every position as the reciprocal value of how often this k-mer occurs approximately in the genome, i.e. with up to e mismatches.

Results

We present a fast method GenMap to compute the (k, e)-mappability. We extend the mappability algorithm, such that it can also be computed across multiple genomes where a k-mer occurrence is only counted once per genome. This allows for the computation of marker sequences or finding candidates for probe design by ide

SUBMITTER: Pockrandt C 

PROVIDER: S-EPMC7320602 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature