alignoth-0.2.2 is not a library.

alignoth

A tool for creating alignment plots from bam files. The generated vega-lite plots are written to stdout per default.

Usage

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 bamboo:

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
output	-o	If present, data and vega-lite specs of the generated plot will be split and written to the given directory
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

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