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. 2019 Mar 13;9:4318. doi: 10.1038/s41598-019-40739-8

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© The Author(s) 2019

Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Effect of using partitioned indexes versus a single reference index on alignment quality. (a) Base-level and (b) locus- or block-level alignment accuracy from synthetic long reads. The x-axis shows the error rate of alignments in log scale (see Materials and methods). The y-axis shows the fraction of aligned reads out of all input reads. Each point in the plot corresponds to a mapping quality threshold that varies from 0 (top right) to 60 (bottom left). These plots are akin to precision-recall plots with the x-axis inverted. (c and d) Alignment statistics for Nanopore whole genome sequencing data from NA12878¹⁴ using a 16-part index. (c) The number of total entries (primary + secondary + unaligned) for single-idx, 16-part-idx-merged, and 16-part-idx-no-merge, in log scale. The dotted horizontal line represents the number of reads. (d) Number of primary mappings in function of Minimap2 mapping quality (log scale).