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

Massively parallel sequencing techniques have revolutionized biological andmedical sciences by providing unprecedented insight into the genomes of humans,animals, and microbes. Modern sequencing platforms generate enormous amounts ofgenomic data in the form of nucleotide sequences or reads. Aligning reads ontoreference genomes enables the identification of individual-specific geneticvariants and is an essential step of the majority of genomic analysispipelines. Aligned reads are essential for answering important biologicalquestions, such as detecting mutations driving various human diseases andcomplex traits as well as identifying species present in metagenomic samples.The read alignment problem is extremely challenging due to the large size ofanalyzed datasets and numerous technological limitations of sequencingplatforms, and researchers have developed novel bioinformatics algorithms totackle these difficulties. Importantly, computational algorithms have evolvedand diversified in accordance with technological advances, leading to todaysdiverse array of bioinformatics tools. Our review provides a survey ofalgorithmic foundations and methodologies across 107 alignment methodspublished between 1988 and 2020, for both short and long reads. We providerigorous experimental evaluation of 11 read aligners to demonstrate the effectof these underlying algorithms on speed and efficiency of read aligners. Weseparately discuss how longer read lengths produce unique advantages andlimitations to read alignment techniques. We also discuss how general alignmentalgorithms have been tailored to the specific needs of various domains inbiology, including whole transcriptome, adaptive immune repertoire, and humanmicrobiome studies.

Technology dictates algorithms: Recent developments in read alignment