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Karel Břinda

Publications and source records attributed to Karel Břinda.

7 recordsLinked to original sources
arXiv2018

Ococo: an online variant and consensus caller

Motivation: Identifying genomic variants is an essential step for connecting genotype and phenotype. The usual approach consists of statistical inference of variants from alignments of sequencing reads. State-of-the-art variant callers can resolve a wide range of different variant types with high accuracy. However, they require that all read alignments be available from the beginning of variant calling and be sorted by coordinates. Sorting is computationally expensive, both memory- and speed-wise, and the resulting pipelines suffer from storing and retrieving large alignments files from external memory. Therefore, there is interest in developing methods for resource-efficient variant calling. Results: We present Ococo, the first program capable of inferring variants in a real-time, as read alignments are fed in. Ococo inputs unsorted alignments from a stream and infers single-nucleotide variants, together with a genomic consensus, using statistics stored in compact several-bit counters. Ococo provides a fast and memory-efficient alternative to the usual variant calling. It is particularly advantageous when reads are sequenced or mapped progressively, or when available computational resources are at a premium.

q-bio.GN↗
arXiv2016

Dynamic read mapping and online consensus calling for better variant detection

Variant detection from high-throughput sequencing data is an essential step in identification of alleles involved in complex diseases and cancer. To deal with these massive data, elaborated sequence analysis pipelines are employed. A core component of such pipelines is a read mapping module whose accuracy strongly affects the quality of resulting variant calls. We propose a dynamic read mapping approach that significantly improves read alignment accuracy. The general idea of dynamic mapping is to continuously update the reference sequence on the basis of previously computed read alignments. Even though this concept already appeared in the literature, we believe that our work provides the first comprehensive analysis of this approach. To evaluate the benefit of dynamic mapping, we developed a software pipeline (http://github.com/karel-brinda/dymas) that mimics different dynamic mapping scenarios. The pipeline was applied to compare dynamic mapping with the conventional static mapping and, on the other hand, with the so-called iterative referencing - a computationally expensive procedure computing an optimal modification of the reference that maximizes the overall quality of all alignments. We conclude that in all alternatives, dynamic mapping results in a much better accuracy than static mapping, approaching the accuracy of iterative referencing. To correct the reference sequence in the course of dynamic mapping, we developed an online consensus caller named OCOCO (http://github.com/karel-brinda/ococo). OCOCO is the first consensus caller capable to process input reads in the online fashion. Finally, we provide conclusions about the feasibility of dynamic mapping and discuss main obstacles that have to be overcome to implement it. We also review a wide range of possible applications of dynamic mapping with a special emphasis on variant detection.

q-bio.GN↗
arXiv2016

Blind Friendly Maps: Tactile Maps for the Blind as a Part of the Public Map Portal (Mapy.cz)

Blind people can now use maps located at Mapy.cz, thanks to the long-standing joint efforts of the ELSA Center at the Czech Technical University in Prague, the Teiresias Center at Masaryk University, and the company Seznam.cz. Conventional map underlays are automatically adjusted so that they could be read through touch after being printed on microcapsule paper, which opens a whole new perspective in the use of tactile maps. Users may select an area of their choice in the Czech Republic (only within its boundaries, for the time being) and also the production of tactile maps, including the preparation of the map underlays, takes no more than several minutes.

cs.HC↗
arXiv2015

RNF: a general framework to evaluate NGS read mappers

Aligning reads to a reference sequence is a fundamental step in numerous bioinformatics pipelines. As a consequence, the sensitivity and precision of the mapping tool, applied with certain parameters to certain data, can critically affect the accuracy of produced results (e.g., in variant calling applications). Therefore, there has been an increasing demand of methods for comparing mappers and for measuring effects of their parameters. Read simulators combined with alignment evaluation tools provide the most straightforward way to evaluate and compare mappers. Simulation of reads is accompanied by information about their positions in the source genome. This information is then used to evaluate alignments produced by the mapper. Finally, reports containing statistics of successful read alignments are created. In default of standards for encoding read origins, every evaluation tool has to be made explicitly compatible with the simulator used to generate reads. In order to solve this obstacle, we have created a generic format RNF (Read Naming Format) for assigning read names with encoded information about original positions. Futhermore, we have developed an associated software package RNF containing two principal components. MIShmash applies one of popular read simulating tools (among DwgSim, Art, Mason, CuReSim etc.) and transforms the generated reads into RNF format. LAVEnder evaluates then a given read mapper using simulated reads in RNF format. A special attention is payed to mapping qualities that serve for parametrization of ROC curves, and to evaluation of the effect of read sample contamination.

q-bio.GN↗
arXiv2014

Balances of $m$-bonacci words

The $m$-bonacci word is a generalization of the Fibonacci word to the $m$-letter alphabet $\mathcal{A} = {0,...,m-1}$. It is the unique fixed point of the Pisot--type substitution $ φ_m: 0\to 01, 1\to 02, ..., (m-2)\to0(m-1), and (m-1)\to0$. A result of Adamczewski implies the existence of constants $c^{(m)}$ such that the $m$-bonacci word is $c^{(m)}$-balanced, i.e., numbers of letter $a$ occurring in two factors of the same length differ at most by $c^{(m)}$ for any letter $a\in \mathcal{A}$. The constants $c^{(m)}$ have been already determined for $m=2$ and $m=3$. In this paper we study the bounds $c^{(m)}$ for a general $m\geq2$. We show that the $m$-bonacci word is $(\lfloor κm \rfloor +12)$-balanced, where $κ\approx 0.58$. For $m\leq 12$, we improve the constant $c^{(m)}$ by a computer numerical calculation to the value $\lceil\frac{m+1}{2}\rceil$.

math.CO↗
arXiv2014

Languages of lossless seeds

Several algorithms for similarity search employ seeding techniques to quickly discard very dissimilar regions. In this paper, we study theoretical properties of lossless seeds, i.e., spaced seeds having full sensitivity. We prove that lossless seeds coincide with languages of certain sofic subshifts, hence they can be recognized by finite automata. Moreover, we show that these subshifts are fully given by the number of allowed errors k and the seed margin l. We also show that for a fixed k, optimal seeds must asymptotically satisfy l ~ m^(k/(k+1)).

cs.DM↗