Table 3 Alignment tools
From: Unraveling genomic variation from next generation sequencing data
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 |  |  |