Semantic Scholar Open Access 2020 120 sitasi

Technology dictates algorithms: recent developments in read alignment

M. Alser Jeremy Rotman Dhrithi Deshpande Kodi Taraszka Huwenbo Shi +12 lainnya

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Abstrak

Aligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines. Computational algorithms for read alignment have evolved in accordance with technological advances, leading to today’s diverse array of alignment methods. We provide a systematic survey of algorithmic foundations and methodologies across 107 alignment methods, for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. We discuss how general alignment algorithms have been tailored to the specific needs of various domains in biology.

Topik & Kata Kunci

Medicine Biology

Penulis (17)

M. Alser

Jeremy Rotman

Dhrithi Deshpande

Kodi Taraszka

Huwenbo Shi

P. Baykal

H. Yang

Victor Xue

S. Knyazev

Benjamin D. Singer

B. Balliu

D. Koslicki

P. Skums

A. Zelikovsky

C. Alkan

O. Mutlu

S. Mangul

Format Sitasi

APA MLA BibTeX

Alser, M., Rotman, J., Deshpande, D., Taraszka, K., Shi, H., Baykal, P. et al. (2020). Technology dictates algorithms: recent developments in read alignment. https://doi.org/10.1186/s13059-021-02443-7

Akses Cepat

Lihat di Sumber doi.org/10.1186/s13059-021-02443-7

Informasi Jurnal

Tahun Terbit: 2020
Bahasa: en
Total Sitasi: 120×
Sumber Database: Semantic Scholar
DOI: 10.1186/s13059-021-02443-7
Akses: Open Access ✓