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. 2020 Jul 29;11:1807. doi: 10.3389/fmicb.2020.01807

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Copyright © 2020 Fouret, Brunet, Binet, Aurine, Enchéry, Croze, Guinier, Goumaidi, Preininger, Volff, Bailly-Bechet, Lachuer, Horvat and Legras-Lachuer.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Integrating phylogenetic and gene-based secondary scaffolding with Scaff2links. Scaff2link allows the import of linkages established by both AGOUTI for gene-based scaffolding and Ragout for reference-assisted scaffolding (see section “Materials and Methods”). The results of the process of conservative union from (1) the initial state with links parsed from Ragout and AGOUTI to (2) the linear chain simplification and (3) the directed acyclic graph simplification is respectively shown on (A), (B), and (C) were connected components resolved up to a single node are no longer displayed. One connected component at the initial step 1, 2, and 3 are respectively shown on (D), (E), and (C) and highlighted in blue. Graph structure and different steps (1–3) are detailed in Supplementary Material.