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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Suitability of Different Mapping Algorithms for Genome-Wide Polymorphism Scans with Pool-Seq Data.
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Massive haplotypes underlie ecotypic differentiation in sunflowers
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TL;DR: Re-sequencing of 1506 wild sunflowers from three species identified 37 large, non-recombining haplotype blocks associated with numerous ecologically relevant traits, and soil and climate characteristics, which highlight a pervasive role of structural variation in maintaining complex ecotypic adaptation.
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