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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