TY - JOUR
T1 - GenMap
T2 - ultra-fast computation of genome mappability
AU - Pockrandt, Christopher
AU - Alzamel, Mai
AU - Iliopoulos, Costas S.
AU - Reinert, Knut
PY - 2020/3/31
Y1 - 2020/3/31
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85087320301&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btaa222
DO - 10.1093/bioinformatics/btaa222
M3 - Article
C2 - 32246826
AN - SCOPUS:85087320301
SN - 1367-4811
VL - 36
SP - 3687
EP - 3692
JO - Bioinformatics (Oxford, England)
JF - Bioinformatics (Oxford, England)
IS - 12
ER -