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MOTIVATION During the past years, next-generation sequencing has become a key technology for many applications in the biomedical sciences. Throughput continues to increase and new protocols provide longer reads than currently available. In almost all applications, read mapping is a first step. Hence, it is crucial to have algorithms and implementations that(More)
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(More)
We present a simple randomized data structure for two-dimensional point sets that allows fast nearest neighbor queries in many cases. An implementation outperforms several previous implementations for commonly used benchmarks.)} of n points in two-dimensional Euclidean space, we want to build a linear space data structure that can answer nearest neighbor(More)
MOTIVATION Automatic error correction of high-throughput sequencing data can have a dramatic impact on the amount of usable base pairs and their quality. It has been shown that the performance of tasks such as de novo genome assembly and SNP calling can be dramatically improved after read error correction. While a large number of methods specialized for(More)
We describe an approach to parallel graph partitioning that scales to hundreds of processors and produces a high solution quality. For example, for many instances from Walshaw's benchmark collection we improve the best known partitioning. We use the well known framework of multi-level graph partitioning. All components are implemented by scalable parallel(More)
Recent advances in rapid, low-cost sequencing have opened up the opportunity to study complete genome sequences. The computational approach of multiple genome alignment allows investigation of evolutionarily related genomes in an integrated fashion, providing a basis for downstream analyses such as rearrangement studies and phylogenetic inference. Graphs(More)
MOTIVATION Large insertions of novel sequence are an important type of structural variants. Previous studies used traditional de novo assemblers for assembling non-mapping high-throughput sequencing (HTS) or capillary reads and then tried to anchor them in the reference using paired read information. RESULTS We present approaches for detecting insertion(More)
We propose the simple method HLA-MA for consistency checking in pipelines operating on human HTS data. The method is based on the HLA typing result of the state-of-the-art method Opti-Type. Provided that there is sufficient coverage of the HLA loci, comparing HLA types allows for simple , fast, and robust matching of samples from whole genome, exome, and(More)
In this section, we describe some more involved details of the benchmark. We note that each match with distance ≤ k − 2 implies at least one match on both sides of it. Figure 1 in the main article shows an example. This can also be seen in Figure 2 in the main article. For k = 5, the third end position of the third lower branch in the left tree implies(More)