Open Access

Erratum to: A representation of a compressed de Bruijn graph for pan-genome analysis that enables search

Algorithms for Molecular Biology201611:28

https://doi.org/10.1186/s13015-016-0090-8

Received: 9 November 2016

Accepted: 9 November 2016

Published: 28 November 2016

The original article was published in Algorithms for Molecular Biology 2016 11:20

Erratum to: Algorithms Mol Biol (2016) 11:20 DOI 10.1186/s13015-016-0083-7

After publication of the original article [1], the authors noticed errors in Algorithm 2 and the caption of Table 4. In Algorithm 2, the term “rank1(Bl, i − 1) + 1” should be included on line 28 and not line 29. In addition, in the caption of Table 4, the word “BVr” should be replaced by “Br” and the word “BVl” should be replaced by “Bl”. The correct versions of Algorithm 2 and Table 4 are included in this erratum.
Table 4

Breakdown of the space usage of the variants of Algorithm A4

Algorithm

Part

62 E.coli

7 × Chr1

7 × HG

A4

wt-bwt

0.42 (23.83%)

0.44 (36.23%)

0.43 (22.68%)

A4

Nodes

0.10 (5.94%)

0.03 (2.61%)

0.04 (2.02%)

A4

\(B_r\)

0.16 (8.93%)

0.16 (12.86%)

0.16 (8.25%)

A4

\(B_l\)

0.14 (8.04%)

0.14 (11.57%)

0.14 (7.42%)

A4

wt-doc

0.93 (53.26%)

0.45 (36.73%)

1.13 (59.63%)

A4compr1

wt-bwt

0.42 (28.57%)

0.44 (47.83%)

0.43 (26.85%)

A4compr1

Nodes

0.10 (7.12%)

0.03 (3.44%)

0.04 (2.39%)

A4compr1

\(B_r\)

0.00 (0.23%)

0.00 (0.12%)

0.00 (0.09%)

A4compr1

\(B_l\)

0.00 (0.23%)

0.00 (0.12%)

0.00 (0.08%)

A4compr1

wt-doc

0.93 (63.85%)

0.45 (48.49%)

1.13 (70.59%)

A4compr2

wt-bwt

0.16 (13.03%)

0.22 (31.01%)

0.22 (15.62%)

A4compr2

Nodes

0.10 (8.67%)

0.03 (4.55%)

0.04 (2.76%)

A4compr2

\(B_r\)

0.00 (0.28%)

0.00 (0.16%)

0.00 (0.10%)

A4compr2

\(B_l\)

0.00 (0.28%)

0.00 (0.16%)

0.00 (0.10%)

A4compr2

wt-doc

0.93 (77.74%)

0.45 (64.11%)

1.13 (81.42%)

The first column shows the algorithm used in the experiment (the k-mer size is 50). The second column specifies the different data structures used: wt-bwt stands for the wavelet tree of the \(\mathsf {BWT}\) (including rank and select support), nodes stands for the array of nodes (the implicit graph representation), \(B_r\) and \(B_l\) are the bit vectors described in “Computation of right-maximal k-mers and node identifiers” section (including rank support), and wt-doc stands for the wavelet tree of the document array. The remaining columns show the memory usage in bytes per base pair and, in parentheses, their percentage

Notes

Declarations

Open AccessThis 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.

Authors’ Affiliations

(1)
Institute of Theoretical Computer Science, Ulm University

Reference

  1. Beller T, Ohlebusch E. A representation of a compressed de Bruijn graph for pan-genome analysis that enables search. Algorithms Mol Biol. 2016;11:20. doi:10.1186/s13015-016-0083-7.View ArticlePubMedPubMed CentralGoogle Scholar

Copyright

© The Author(s) 2016

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