java -mx512m -jar BamView.jar

and extra command line options are given when '-h' is used:

java -jar BamView.jar -h

BAM files can be specified on the command line with the '-a' option:

java -mx512m -jar BamView.jar -a pathToFile/sorted.bam

If a BAM filename is not given on the command line BamView will prompt for a file to be entered. The BAM index file should have the same name as the BAM file but with a '.bai' suffix. Multiple BAM files can be loaded and overlaid in the viewer. To make this easier BamView will read in files that contain a list of filenames.

Address of the bookmark: http://bamview.sourceforge.net/

https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbaf208/8257678?login=true

Address of the bookmark: https://github.com/sib-swiss/termal

Tutorial http://shinycircos.ncpgr.cn/shinyCircos_Help_Manual.pdf

Github https://github.com/venyao/shinyCircos

Address of the bookmark: http://150.109.59.144:3838/shinyCircos/

Dot supports the output of MUMmer’s nucmer aligner the most commonly used software method for aligning genome assemblies. A quick script called DotPrep.py converts the delta file to a more streamlined coordinates file with an index that enables Dot to read in more alignments in certain regions on demand.

Dot, an interactive viewer for genome-genome comparison

https://dnanexus.github.io/dot/

Address of the bookmark: https://github.com/dnanexus/dot

BioCircos.js provides SNP, CNV, HEATMAP, LINK, LINE, SCATTER, ARC, TEXT, and HISTGRAMmodules to display genome-wide genetic variations (SNPs, CNVs and chromosome rearrangement), gene expression and biomolecule interactions. BioCircos.js also provides BACKGROUND module to display background and axis circles. Tooltips showing detailed information of SVG elements are also provided.

Demo

Address of the bookmark: http://bioinfo.ibp.ac.cn/biocircos/document/index.html

live demo

Address of the bookmark: https://github.com/rjchallis/codon-usage

Please report new whole genome alignment tools under comment sections.

Address of the bookmark: http://www.cs.utoronto.ca/~brudno/721.full.pdf

Chimeric Alignment: An alignment of a read that cannot be represented as a linear alignment. Typically, one of the linear alignments in a chimeric alignment is considered the “representative” alignment, and the others are called “supplementary” and are distinguished by the supplementary alignment flag.

Chimeric reads are indicative of structural variation in DNA-seq and it may indicate the presence of chimeric genes in RNA-seq.

In short, chimeric reads can be split in to two or more parts, each part would be mapped to reference(it’s not hard-clipped), the total length of the mapped part is longger than read length.

Representative alignment: A chimeric alignment that is represented as a set of linear alignments that do not have large overlaps typically has one linear alignment that is considered the representative alignment.

One read can align to multiple positions, we can find one alignmnet position which sequence do not have large overlaps, it called representative alighment, for other alignment positions, we called them supplementary alignment.

It seems that GATK can realignment those representative reads to the correctly position via RealignerTargetCreator and IndelRealigner. (WARNING: I am not quite sure if I understand this correctly. If someone could help me, please leave me a message below, thanks, thanks.)

Supplementary Alignment: A chimeric reads but not a representative reads.

Primary Alignment and Secondary Alignment: A read may map ambiguously to multiple locations, e.g. due to repeats. Only one of the multiple read alignments is considered primary, and this decision may be arbitrary. All other alignments have the secondary alignment flag.