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GenMap: ultra-fast computation of genome mappability

Research output: Contribution to journalArticle

Christopher Pockrandt, Mai Alzamel, Costas S. Iliopoulos, Knut Reinert

Original languageEnglish
Pages (from-to)3687-3692
Number of pages6
JournalBioinformatics (Oxford, England)
Volume36
Issue number12
DOIs
Published31 Mar 2020

King's Authors

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 identifying approximate k-mers that are unique to a genome or that are present in all genomes. GenMap supports different formats such as binary output, wig and bed files as well as csv files to export the location of all approximate k-mers for each genomic position.

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