NextGenMap: Fast and accurate read mapping in highly polymorphic genomes
TLDR
NextGenMap is reported, a fast and accurate read mapper, which aligns reads reliably to a reference genome even when the sequence difference between target and reference genome is large, i.e. highly polymorphic genome.Abstract:
Summary: When choosing a read mapper, one faces the trade off between speed and the ability to map reads in highly polymorphic regions. Here, we report NextGenMap, a fast and accurate read mapper, which reduces this dilemma. NextGenMap aligns reads reliably to a reference genome even when the sequence difference between target and reference genome is large, i.e. highly polymorphic genome. At the same time, NextGenMap outperforms current mapping methods with respect to runtime and to the number of correctly mapped reads. NextGenMap efficiently uses the available hardware by exploiting multi-core CPUs as well as graphic cards (GPUs), if available. In addition, NextGenMap handles automatically any read data independent of read length and sequencing technology. Availability: NextGenMap source code and documentation are available at: http://cibiv.github.io/NextGenMap/ Contact: fritz.sedlazeck@univie.ac.at Supplementary information: Supplementary data are available at Bioinformatics online.read more
Citations
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Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species.
Sara Kurland,Christopher W. Wheat,Maria de la Paz Celorio Mancera,Verena E. Kutschera,Jason Hill,Anastasia Andersson,Carl-Johan Rubin,Leif Andersson,Leif Andersson,Leif Andersson,Nils Ryman,Linda Laikre +11 more
TL;DR: The Pool‐seq‐only approach can be suitable for detecting and quantifying genome‐wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.
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Contemporary evolution of maize landraces and their wild relatives influenced by gene flow with modern maize varieties
Idalia Claudia Rojas-Barrera,Ana Wegier,José de Jesús Sánchez González,Gregory L. Owens,Gregory L. Owens,Loren H. Rieseberg,Daniel Piñero +6 more
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Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes
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Sex-Biased Gene Expression and Dosage Compensation on the Artemia franciscana Z-Chromosome.
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TRUmiCount: correctly counting absolute numbers of molecules using unique molecular identifiers
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