Table 1 Comparison to other genomic display tools
From: ContigScape: a Cytoscape plugin facilitating microbial genome gap closing
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) | Â | Â | Â | Â | Â | Â | Â | Â |