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. 2018 Nov 6;19:406. doi: 10.1186/s12859-018-2432-7

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© The Author(s) 2018

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 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.

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Fig. 1 — EIM pipeline overview and applied tools. The first step has three outputs: leftover reads (R^′), modified remaining parts of the genome sequence (G^M) and exact contigs (Cng1). The output of the second step is inexact contig set indicated by Cng2. Currently, EIM can apply one of mappers Bowtie2 [7], BWA [8, 9] and Yara [10] for mapping reads