A tool for creating alignment plots from bam files. The generated vega-lite plots are written to stdout per default. 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
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 | | | highlight | -h | Interval that will be highlighted in the visualization. Example: 132400-132500 | | | 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 | | 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 | |
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