Table 3.
Alignment tools
| Tool | Purpose | Properties | Support | Availability |
|---|---|---|---|---|
| ABySS Explorer [88] |
• Global sequence assemblies from smaller fragments of DNA |
• de-Bruijn directed graphs |
• DOT files [63] |
• Java stand-alone application |
| CLC Genomics workbench |
• Analysis of de novo assembly |
• SNP detection techniques |
• Sanger, 454, Illumina and SOLID |
• Commercial stand-alone application |
|
• genomic rearrangements structural variations | ||||
| EagleView [89] |
• Large genome assemblies |
• Multiple-line scheme |
• Navigation by genomic location, read identifiers, annotations, descriptions, user-defined coordinate map |
• Free stand-alone application |
| Hawkeye [90] |
• Detection of anomalies in data and visually identify and correct assembly errors |
• Consensus validation of potential genes, dynamic filtering and automated clustering |
• Compatibility with Phrap, ARACHNE [34], Celera Assembler [32] and others |
• Free stand-alone application |
| LookSeq [91] |
• Visualization of sequences derived from multiple sequencing technologies |
• Browsing at different resolutions |
• SAM/BAM files |
• Web applicastion |
|
• Read-depth coverage | ||||
|
• Putative single nucleotide and SV | ||||
| MagicViewer [92] |
• Assembly visualization and genetic variation annotation tool mainly developed to easily visualize short read mapping |
• Identification and annotation of genetic variation based on the reference genome |
• Multiple color schemes |
• Pipeline to detect, filter, annotate visualize or classify by function genetic variations |
|
• Zoomable interface | ||||
| MapView [93] |
• Alignments of huge-scale single-end and pair-end short reads |
• Multiple navigation |
• MapView formatted (MVF) files |
• Free stand-alone application |
|
• Zooming modes | ||||
|
• Multi-thread processing | ||||
| • Variation analysis |