id,collection,dc.contributor.author,dc.date.accessioned,dc.date.available,dc.date.issued,dc.description.abstract[en],dc.format.extent,dc.identifier.uri,dc.language,dc.rights.uri,dc.subject,dc.subject.ddc,dc.title,dc.type,dcterms.accessRights.openaire,dcterms.bibliographicCitation,dcterms.bibliographicCitation.doi,dcterms.bibliographicCitation.url,dcterms.isPartOf.issn,refubium.affiliation.other,refubium.affiliation[de],refubium.mycore.derivateId,refubium.mycore.fudocsId,refubium.resourceType.isindependentpub "399473be-b5e8-4867-a1fe-c992df9eb15a","fub188/16","Holtgrewe, Manuel||Emde, Anne-Katrin||Weese, David||Reinert, Knut","2018-06-08T03:37:52Z","2013-08-08T13:18:41.186Z","2011","Background Second generation sequencing technologies yield DNA sequence data at ultra high-throughput. Common to most biological applications is a mapping of the reads to an almost identical or highly similar reference genome. The assessment of the quality of read mapping results is not straightforward and has not been formalized so far. Hence, it has not been easy to compare different read mapping approaches in a unified way and to determine which program is the best for what task. Results We present a new benchmark method, called Rabema (Read Alignment BEnchMArk), for read mappers. It consists of a strict definition of the read mapping problem and of tools to evaluate the result of arbitrary read mappers supporting the SAM output format. Conclusions We show the usefulness of the benchmark program by performing a comparison of popular read mappers. The tools supporting the benchmark are licensed under the GPL and available from http://www.seqan.de/projects/rabema.html.","10 S.","https://refubium.fu-berlin.de/handle/fub188/15594||http://dx.doi.org/10.17169/refubium-19782","eng","http://creativecommons.org/licenses/by/2.0/","Edit Distance||Read Mapper||Tandem Repeat Region||Full Sensitivity||Short Tandem Repeat Region","500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie||000 Informatik, Informationswissenschaft, allgemeine Werke::000 Informatik, Wissen, Systeme::004 Datenverarbeitung; Informatik","A novel and well-defined benchmarking method for second generation read mapping","Wissenschaftlicher Artikel","open access","BMC Bioinformatics 12 (2011), 210","10.1186/1471-2105-12-210","http://doi.org/10.1186/1471-2105-12-210","1471-2105","Institut für Informatik:::6dd1f8be-8a6d-4a4a-8f8d-572eb83788da:::600","Mathematik und Informatik","FUDOCS_derivate_000000002753","FUDOCS_document_000000018725","no"