Table 1

Comparison to other genomic display tools
Program Main display Connections between contigs Connections between scaffolds Compatible assemblers Objects Global contig display The weight of contigs’ relationship Type
Consed Linear From paired reads No Any producing ACE files nonselective No No stand-alone
(Gordon et al., [5])
Phrapview Linear From paired reads No Phrap nonselective No No stand-alone
(Gordon et al., [5])
Gap5 Linear No No All nonselective No No stand-alone
(Bonfield et al., [12])
UCSC Linear No No No nonselective No No stand-alone
(Kent et al., [13])
Ensembl Linear No No No nonselective No No stand-alone
(Stalker et al., [14])
IGV Linear No No All nonselective No No stand-alone
(Robinson et al., [15])
EagleView Linear No No Any producing ACE files nonselective No No stand-alone
(Huang, Marth [16])
Hawkeye Linear From paired reads viewed within a single scaffold No Any producing AFG files nonselective No No stand-alone
(Schatz et al., [17])
ABySS-Explorer Graphs From paired reads No ABySS nonselective One node No stand-alone
(Nielsen et al., [9])
TGNet Graphs From transcripts, From scaffolding information From transcripts All eukaryocyte One node No Perl scripts
(Oksana et al., [10])
ContigScape Graphs From reference, From scaffolding information, 454 repeat reads or other database From reference, From other database All Fungi,,bacteria, plasmid, virus etc. One edge and two nodes display plugin
(the publication)

Tang et al.

Tang et al. BMC Genomics 2013 14:289   doi:10.1186/1471-2164-14-289

Open Data