title: Simultaneous alignment of short reads against multiple genomes.
abstract: Genome resequencing with short reads generally relies on alignments against a single reference. GenomeMapper supports simultaneous mapping of short reads against multiple genomes by integrating related genomes (e.g., individuals of the same species) into a single graph structure. It constitutes the first approach for handling multiple references and introduces representations for alignments against complex structures. Demonstrated benefits include access to polymorphisms that cannot be identified by alignments against the reference alone. Download GenomeMapper at http://1001genomes.org.
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37-39, D-72076 Tübingen, Germany. korbinian.schneeberger@tuebingen.mpg.de
authors.forename: Korbinian
authors.initials: K
authors.lastname: Schneeberger
authors.forename: Jörg
authors.initials: J
authors.lastname: Hagmann
authors.forename: Stephan
authors.initials: S
authors.lastname: Ossowski
authors.forename: Norman
authors.initials: N
authors.lastname: Warthmann
authors.forename: Sandra
authors.initials: S
authors.lastname: Gesing
authors.forename: Oliver
authors.initials: O
authors.lastname: Kohlbacher
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D016678:Genome / Q000235:genetics; D023281:Genomics / Q000379:methods; D008969:Molecular Sequence Data; D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software