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  GenMap: Ultra-fast Computation of Genome Mappability

Pockrandt, C. M., Alzamel, M., Iliopoulos, C. S., & Reinert, K. (2020). GenMap: Ultra-fast Computation of Genome Mappability. Bioinformatics, btaa222. doi:10.1093/bioinformatics/btaa222.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0006-4E29-6 Version Permalink: http://hdl.handle.net/21.11116/0000-0006-4E2A-5
Genre: Journal Article

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 Creators:
Pockrandt, Christopher M.1, Author              
Alzamel, Mai, Author
Iliopoulos, Costas S. , Author
Reinert, Knut2, Author              
Affiliations:
1Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              
2Efficient Algorithms for Omics Data (Knut Reinert), Max Planck Fellow Group, Max Planck Institute for Molecular Genetics, Max Planck Society, ou_2385698              

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 Abstract: Motivation:Computing the uniqueness ofk-mers for each position of a genome while allowing for up toemismatches is computationally challenging. However, it is crucial for many biological applications suchas the design of guide RNA for CRISPR experiments. More formally, the uniqueness or(k, e)-mappabilitycan be described for every position as the reciprocal value of how often thisk-mer occurs approximatelyin the genome, i.e., with up toemismatches.Results:We present a fast method GenMap to compute the(k, e)-mappability. We extend the mappabilityalgorithm, such that it can also be computed across multiple genomes where ak-mer occurrence is onlycounted once per genome. This allows for the computation of marker sequences or finding candidatesfor probe design by identifying approximatek-mers that are unique to a genome or that are present in allgenomes. GenMap supports different formats such as binary output, wig and bed files as well as csv filesto export the location of all approximatek-mers for each genomic position.Availability:GenMap can be installed via bioconda. Binaries and C++ source code are available onhttps://github.com/cpockrandt/genmap.

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Language(s): eng - English
 Dates: 2020-03-252020-04-04
 Publication Status: Published in print
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 Identifiers: DOI: 10.1093/bioinformatics/btaa222
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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: - Sequence Number: btaa222 Start / End Page: - Identifier: ISSN: 1367-4803
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991