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. 2021 Aug 26;22:249. doi: 10.1186/s13059-021-02443-7

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 3 — The landscape of read alignment algorithms published from 1988 to 2020. a Histogram showing the cumulation of surveyed tools over time colored by the algorithm used for genome indexing. The first published aligner, FASTA, is labeled as well as the point at which Bowtie and BWA were introduced and changed the landscape of aligners. b The popularity of all surveyed aligners, judged by citations per year since the initial release. Tools are grouped by the algorithm used for genome indexing. The six overall most popular aligners are labeled. c Histogram showing the cumulation of surveyed tools over time colored by the algorithm used for pairwise alignment. The two aligners credited to have been the first to use the three most popular algorithms (FASTA: Smith-Waterman and Needleman-Wunsch, RMAP: Hamming distance) are labeled. d The popularity of each surveyed aligner, judged by citations per year since the initial release. Tools are grouped by the algorithm used for pairwise alignment. The six overall most popular aligners are labeled.