English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

Aligning reads to a reference sequence is a fundamental step in numerousbioinformatics pipelines. As a consequence, the sensitivity and precision ofthe mapping tool, applied with certain parameters to certain data, cancritically affect the accuracy of produced results (e.g., in variant callingapplications). Therefore, there has been an increasing demand of methods forcomparing mappers and for measuring effects of their parameters.  Read simulators combined with alignment evaluation tools provide the moststraightforward way to evaluate and compare mappers. Simulation of reads isaccompanied by information about their positions in the source genome. Thisinformation is then used to evaluate alignments produced by the mapper.Finally, reports containing statistics of successful read alignments arecreated.  In default of standards for encoding read origins, every evaluation tool hasto be made explicitly compatible with the simulator used to generate reads. Inorder to solve this obstacle, we have created a generic format RNF (Read NamingFormat) for assigning read names with encoded information about originalpositions.  Futhermore, we have developed an associated software package RNF containingtwo principal components. MIShmash applies one of popular read simulating tools(among DwgSim, Art, Mason, CuReSim etc.) and transforms the generated readsinto RNF format. LAVEnder evaluates then a given read mapper using simulatedreads in RNF format. A special attention is payed to mapping qualities thatserve for parametrization of ROC curves, and to evaluation of the effect ofread sample contamination.

RNF: a general framework to evaluate NGS read mappers