alignoth

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 supports an interactive mode that can be activated by simply executing it without any arguments (i.e. alignoth). This launches a wizard that guides you through selecting input files, defining the region of interest, and choosing between an interactive HTML output or a Vega-Lite specification.

Usage

alignoth

To activate the interactive mode guiding you through the process of creating an alignment plot.

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

Arguments

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 | Named intervals or single base positions that will be highlighted in the visualization. Example: myinterval:132400-132500 or myvariant:132440 | | | vcf | -v | Path to a VCF file. Variants from the VCF file will be highlighted in the resulting plot similar to the highlight option. | | | bed | -b | Path to a BED file. Regions from the BED file will be highlighted in the resulting plot similar to the highlight option. | | | 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 | | | coverage-data-output | | If present coverage 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 | | | no-embed-js | | If present, the generated html will not embed javscript dependencies and therefore be considerably smaller but require internet access to load the dependencies. | false | | around-vcf-record | -a | Plots a region around a specified VCF record taken via its index from the VCF file given via the --vcf option. | | | mismatch-display-min-percent | | The minimum percentage of mismatches to display in the coverage plot. | 1 |

Installation

There a multiple ways to install alignoth:

Pixi

Alignoth can be easily installed globally using pixi:

pixi global install alignoth

Bioconda

Rust-Bio-Tools is available via Bioconda. With Bioconda set up, installation is as easy as

conda install alignoth -c conda-forge -c bioconda -c nodefaults

Pay attention to the correct channel ordering for the installation.

Cargo

If the Rust compiler and associated Cargo are installed, alignoth may be installed via

cargo install alignoth

Source

Download the source code and within the root directory of source run

cargo install

Authors

• Felix Wiegand
• Johannes Köster (https://koesterlab.github.io)