title: leeHom: adaptor trimming and merging for Illumina sequencing reads.
abstract: The sequencing of libraries containing molecules shorter than the read length, such as in ancient or forensic applications, may result in the production of reads that include the adaptor, and in paired reads that overlap one another. Challenges for the processing of such reads are the accurate identification of the adaptor sequence and accurate reconstruction of the original sequence most likely to have given rise to the observed read(s). We introduce an algorithm that removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach. Our algorithm is faster, and provides a more accurate reconstruction of the original sequence for both simulated and ancient DNA data sets, than other approaches. leeHom is released under the GPLv3 and is freely available from: https://bioinf.eva.mpg.de/leehom/
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Renaud
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
authors.forename: Udo
authors.initials: U
authors.lastname: Stenzel
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany kelso@eva.mpg.de.
authors.forename: Janet
authors.initials: J
authors.lastname: Kelso
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D016013:Likelihood Functions; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
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