From: GenomeGems: evaluation of genetic variability from deep sequencing data
Tool | View | Data integration |
---|---|---|
ABC[14] | Three distinct display modes: | NA |
1. A very low resolution- histogram | ||
2. Intermediate resolutions- a ‘Wiggly Plot’ | ||
3. Very high resolution - the user may view the sequence data directly. | ||
EagleView[15] | Compact with zooming capability. | Genome features (exon, intron, etc.), Polymorphism data (e.g. SNP), 454 flowgram trace, Illumina four color raw signals. |
Pinpoint view of: base quality, technology-specific sequence trace, read ID and strand. | ||
LookSeq[16] | 1. A resolution from the level of a whole chromosome to the level of individual bases. | LookSeq can visualize read alignments and some basic properties as separate “tracks”: |
2. There are options to view genome coverage, GC content, and annotations to the reference sequence. | 1. Sequence annotation | |
2. Coverage | ||
3. GC contents | ||
This information is taken from the alignment databases as well as some auxiliary files. | ||
Magic Viewer[17] | The short read image can be zoomed to any resolution, from a whole chromosome to individual bases at any desired level. | NA |
Also displays auxiliary information: read ID, location, base quality, read length and orientation. | ||
Tablet[18] | The main display provides a view of a single contig at a time, with reads aligned against their consensus sequence. | NA |
GenomeGems | Five separate analysis methods are available: | GenomeGems integrates well with the UCSC Genome Browser, for the purpose of visualization of SNPs, in addition to the analysis and visualization in the actual tool. |
1. Data Table - displays the data supplied by the user and analyzes the percentage of mutant reads, in spreadsheet format, enabling analysis within the tool in addition to fast export to Excel. | UCSC custom tracks supply additional data calculated by UCSC such as: context of the SNP – CDS or intron, and the properties of the changed amino acid – polarity, acidity and hydropathy. | |
2. Sample Comparison - displays a bar graph presenting the frequency of each SNP in the investigated samples, according to a threshold value. | ||
3. SNP-View - displays a table containing the numbers of samples that include each SNP in a specific chromosome. | ||
4. Translation of the input file into a PgSNP file format for a later visualization in the UCSC, as a UCSC Custom Track. | ||
5. Additional Information- suggests additional external links for further investigation and annotation of specific SNPs and of the impact of amino acid changes on human proteins. |