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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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Peak memory usage and runtime for a partitioned index of the human genome. (a) Peak memory usage in function of the number of partitions for ab initio index generation (left) and loading a pre-built index (right). Dark bars represent memory usage when performing chromosome balancing as described herein, whilst light bars represent the default iterative partition distribution as implemented in Minimap2. (b) Detailed runtime metrics for index building across two computational systems. System 1 is a laptop with flash memory (Intel i7-8750H processor, 16 GB of RAM and Toshiba XG5 series NVMe SSD) while system 2 is a workstation with a mechanical hard disk (Intel i7-6700 processor, 16 GB of RAM and Toshiba DT01ACA series HDD). The total indexing time has been broken down into three steps; chr balancing, index building and index concatenations. Chr balancing includes the overhead for chromosome sorting, partitioning and writing each partition to a separate file. (c) Runtime for base-level alignment (left) and block/locus level mapping (right). System 1 and 2 are as described in (b). Alignment was performed on the NA12878 data (see Materials and methods) with the map-ont pre-set in Minimap2 using 8 threads. Runtime statistics are composed of indexing (index generation including the overhead), mapping (total time for aligning reads to each partition), and merging using the method described herein. Runtimes include file reading and writing.