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. 2016 Dec;26(12):1710–1720. doi: 10.1101/gr.209247.116

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© 2016 Carvalho et al.; Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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Figure 3. — Sensitivity and specificity of read overlap detection with masking of repetitive k-mers. Simulated PacBio reads from D. melanogaster (1000 pairs of 10-kb sequences with 2-kb overlaps) were subjected to standard MHAP (blue), MHAP with masking of low-frequency k-mers (red), or MHAP with masking of low-frequency and high-frequency k-mers (black). Note that masking of low- and high-frequency k-mers cause a huge improvement in specificity (right) with minimal losses in sensitivity (left). The reference list of valid k-mers came from Illumina reads.