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Table 1 Comparison of pan-genome tools. We analyzed tools for pan-genome analysis that are available or currently under development. This table lists the corresponding publications or websites. We compared the intended use cases of the tools and the prerequisite data required in order to use them. We evaluated the availability of features needed to work with the pan-genome in subsequent analyses, e.g. updating the set of included genomes. Furthermore, we assessed whether the proposed data structures take into account structural variants and whether it is possible to visualize the resulting pan-genome

From: seq-seq-pan: building a computational pan-genome data structure on whole genome alignment

Name Objective Input Visualization Structural Functionality
    of pan-genome Variants Update Possibility to
      Add Remove include annotation
svaha [9] Graph construction Reference sequence + variants External Yes No No No
cdbg [2] Graph construction Multiple reference sequences External Yes No No No
cdbg_search [6] Graph construction Multiple reference sequences External Yes No No No
SplitMEM [44] Graph construction Multiple reference sequences External Yes No No No
TwoPaCo [7] Graph construction Multiple reference sequences External Yes No No No
GCSA2 [8] Graph indexing Variation graph No No No No No
GCSA [10] Graph indexing Reference sequence + variants No No No No No
  Multiple sequence mapping       
BWBBLE [11] Multiple sequence mapping Reference sequence + variants No No No No No
GenomeMapper [12] Multiple sequence mapping Reference sequence + variants No No No No No
panVC [14] Multiple sequence variant detection Whole genome alignment External Yes No No Yes
MHC-PRG [13] Multiple sequence variant detection Multiple sequence alignment No No Yes No No
  Pan-genome data structure AND variants      
GenomeRing [3] Pan-genome data structure Whole genome alignment Yes Yes No No Yes
JST [15] Pan-genome data structure Reference sequence + variants No Yes Yes Yes Yes
vg [17] Pan-genome data structure Reference sequence + variants External Yes Yes* Yes* Yes
   OR multiple reference sequences      
PanCake [16] Pan-genome data structure Multiple reference sequences External Yes Yes No No
   AND pairwise alignment      
seq-seq-pan Pan-genome data structure Multiple reference sequences External Yes Yes Yes Yes
  1. Adding and removing of genomes in vg can be achieved using a combination of several steps