Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which leads to better results. But sometime, we need publication ready figure of genomes. Following are the list of genome alignment visualization tools, which could be useful for analysis and interpretation of results:
ABySS Explorer
Interactive Java application that uses a novel graph-based representation to display a sequence assembly and associated metadata
http://www.bcgsc.ca/platform/bioinfo/software/abyss-explorer
BamView
Genome browser and annotation tool that allows visualization of sequence features, next-generation sequencing (NGS) data and the results of analyses within the context of the sequence, and also its six-frame translation
http://www.sanger.ac.uk/resources/software/artemis/
DNannotator
Annotation web toolkit for regional genomic sequences
http://bioapp.psych.uic.edu/DNannotator.htm
JVM
Java Visual Mapping tool for NGS reads
LookSeq
Web-based visualization of sequences derived from multiple sequencing technologies. Low- or high-depth read pileups and easy visualization of putative single nucleotide and structural variation
http://lookseq.sourceforge.net
MagicViewer
Visualization of short read alignment, identification of genetic variation and association with annotation information of a reference genome
http://bioinformatics.zj.cn/magicviewer/
MapView
Alignments of huge-scale single-end and pair-end short reads
http://omictools.com/mapview-s1367.html
MultiPipMaker
Computes alignments of similar regions in two DNA sequences. The resulting alignments are summarized with a ‘percent identity plot’ (pip)
http://pipmaker.bx.psu.edu/pipmaker/
PileLineGUI
Handling genome position files in NGS studies
http://sing.ei.uvigo.es/pileline/pilelinegui.html
SAMtools tview
Simple and fast text alignment viewer; NGS compatible
SEWAL
Uses a locality-sensitive hashing algorithm to enumerate all unique sequences in an entire Illumina sequencing run
http://www.sourceforge.net/projects/sewal
STAR
A web-based integrated solution to management and visualization of sequencing data
http://wanglab.ucsd.edu/star/browser
SVA
Software for annotating and visualizing sequenced human genomes
Viewer (IGV)
Visualization of large heterogeneous datasets, providing a smooth and intuitive user experience at all levels of genome resolution
https://www.broadinstitute.org/igv/
ZOOM Lite
NGS data mapping and visualization software
