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A number of collected useful next-generation data analyis software can be accessed from SEQanswers forums
 Next-generation sequencing data visualization tools
 EagleView
EagleView is an information-rich genome assembler viewer. It can display a dozen different types of information including base quality and flowgram signal. Developers at Boston College.
 LookSeq
LookSeq is a web-based application for alignment visualization, browsing and analysis of genome sequence data. It supports multiple sequencing technologies, alignment sources, and viewing modes; low or high-depth read pileups; and easy visualization of putative single nucleotide and structural variation. From the Sanger Centre.
 MapView
MapView is a visualization tool for short reads alignment on desktop computer. From the Evolutionary Genomics Lab at Sun-Yat Sen University, China.
 NGSView
NGSView is an extensible open source sequence editor to allow for visualization and manipulation of massive amount of sequence data. From RIKEN Omics Science Center, RIKEN Yokohama Institute 1-7-22 Suehiro-cho, Japan
 XMatchView
A visual tool for analyzing cross_match alignments. Developed by Rene Warren and Steven Jones at Canada's Michael Smith Genome Sciences Centre.
 Tablet
A lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments, which supports a range of input assembly formats.
 inGAP
An integrated next-generation genome analysis pipeline to detect single nucleotide polymorphisms (SNPs) and insertion/deletions (indels).
 BamView
An easy Java application for visualising the large amounts of data stored for sequence reads which are aligned against a reference genome sequence based on BAM file.

 

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