Table 3.
Visualization tools for genome alignments
| Tool and references | Description | URL |
|---|---|---|
| ABySS Explorer [210] | 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 [211] | 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 [212] | Annotation web toolkit for regional genomic sequences | http://bioapp.psych.uic.edu/DNannotator.htm |
| JVM [213] | Java Visual Mapping tool for NGS reads | http://www.springer.com/cda/content/document/cda_downloaddocument/9789401792448-c2.pdf?SGWID=0-0-45-1487072-p176815501 |
| LookSeq [214] | 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 [215] | Visualization of short read alignment, identification of genetic variation and association with annotation information of a reference genome | http://bioinformatics.zj.cn/magicviewer/ |
| MapView [216] | Alignments of huge-scale single-end and pair-end short reads | http://omictools.com/mapview-s1367.html |
| MultiPipMaker [217] | 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 [218] | Handling genome position files in NGS studies | http://sing.ei.uvigo.es/pileline/pilelinegui.html |
| SAMtools tview [102] | Simple and fast text alignment viewer; NGS compatible | http://www.htslib.org/ |
| SEWAL [219] | Uses a locality-sensitive hashing algorithm to enumerate all unique sequences in an entire Illumina sequencing run | http://www.sourceforge.net/projects/sewal |
| STAR [220] | A web-based integrated solution to management and visualization of sequencing data | http://wanglab.ucsd.edu/star/browser |
| SVA [221] | Software for annotating and visualizing sequenced human genomes | http://www.svaproject.org |
| Viewer (IGV) [222] | 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 [223] | NGS data mapping and visualization software | http://bioinfor.com/zoom/lite/ |