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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. 2 — The comparison of contigs generated by Bowtie2, Yara and BWA with the respective contigs of EIM on the real read set of E. coli K12. Firstly, the mappers were executed on the read set and the reference, and then the contig sets were generated. Secondly, for each mapper, EIM (v2) was run on the read set and the contig set constructed by the mapper while using it at the second step for mapping. Finally, the contiguity and quality of contigs were computed as a N50 size b Genome-Fraction value c The number of errors d The number of IUPAC codes. In addition, the running time of obtaining contigs was measured and showed in seconds (e)