A tool for creating alignment plots from bam files. The generated vega-lite plots are written to stdout per default. An example of a generated plot can be seen here The name alignoth is derived from the visualized alignments combined with the star alioth (usage of vega plots).
alignoth -b path/to/my.bam -r path/to/my/reference.fa -g chr1:200-300 > plot.vl.json
To directly generate a plot in svg, png or pdf format we advice using the vega-cli and vega-lite-cli packages:
alignoth -b path/to/my.bam -r path/to/my/reference.fa -g chr1:200-300 | vl2vg | vg2pdf > plot.pdf
To generate an interactive view within an html file use --html and capture the output to a file:
alignoth -b path/to/my.bam -r path/to/my/reference.fa -g chr1:200-300 --html > plot.html
The following options are available when using alignoth:
| argument | short | explanation | default |
|---|---|---|---|
| bam-path | -b | The bam file to be visualized. | |
| reference | -r | The path to the reference fasta file | |
| region | -g | Chromosome and region for the visualization. Example: 2:132424-132924 | |
| around | -a | A chromosome and a base position that will define the region that will be plotted starting 500bp before and end 500bp behind the given position. Example: 2:17348 | |
| highlight | -h | Interval or single base position that will be highlighted in the visualization. Example: 132400-132500 or 132440 | |
| plot-all | -p | Plot all reads in the given region. We advise to only use this command for small bam files with a single target. | false |
| max-read-depth | -d | Set the maximum rows of reads that will be shown in the alignment plots | 500 |
| max-width | -w | Set the maximum width of the resulting alignment plot | 1024 |
| output | -o | If present, data and vega-lite specs of the generated plot will be split and written to the given directory | |
| data-format | -f | Sets the output format for the read, reference and highlight data | json |
| aux_tag | -x | Displays the given content of the aux tag in the tooltip of the plot. Multiple usage for more than one tag is possible. | |
| spec-output | If present vega-lite specs will be written to the given file path | ||
| read-data-output | If present read data will be written to the given file path | ||
| ref-data-output | If present reference data will be written to the given file path | ||
| highlight-data-output | If present highlight data will be written to the given file path | ||
| html | If present the generated plot will inserted into a plain html file containing the plot centered which is then written to stdout |
There a multiple ways to install alignoth:
Rust-Bio-Tools is available via Bioconda. With Bioconda set up, installation is as easy as
conda install alignoth
If the Rust compiler and associated Cargo are installed, alignoth may be installed via
cargo install alignoth
Download the source code and within the root directory of source run
cargo install