alignoth 0.6.2

A tool for creating alignment plots from bam files
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71

[![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/koesterlab/alignoth/rust.yml?branch=main&label=tests)](https://github.com/koesterlab/alignoth/actions)
[![codecov](https://codecov.io/gh/koesterlab/alignoth/branch/main/graph/badge.svg?token=G751JNS6PU)](https://codecov.io/gh/koesterlab/alignoth)
[![Bioconda downloads](https://img.shields.io/conda/dn/bioconda/alignoth.svg?style=flat)](http://bioconda.github.io/recipes/alignoth/README.html)
[![Bioconda version](https://img.shields.io/conda/vn/bioconda/alignoth.svg?style=flat)](http://bioconda.github.io/recipes/alignoth/README.html)
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/alignoth/README.html)
[![Licence](https://img.shields.io/conda/l/bioconda/alignoth.svg?style=flat)](http://bioconda.github.io/recipes/alignoth/README.html)

# alignoth

A tool for creating alignment plots from bam files. The generated [vega-lite](https://vega.github.io/vega-lite/) plots are written to stdout per default.
An example of a generated plot can be seen [here](http://htmlpreview.github.io/?https://github.com/koesterlab/alignoth/blob/main/examples/plot.html)
The name alignoth is derived from the visualized **align**ments combined with the star **alioth** (usage of vega plots).
## Usage

```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](https://vega.github.io/vega/usage/#cli) and [vega-lite-cli]( https://vega.github.io/vega-lite/usage/compile.html#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                                                           |         |
| 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                                                                |         |
| html                  |       | If present the generated plot will inserted into a plain html file containing the plot centered which is then written to stdout |         |

## Installation

There a multiple ways to install alignoth:

#### Bioconda

Rust-Bio-Tools is available via [Bioconda](https://bioconda.github.io).
With Bioconda set up, installation is as easy as

    conda install alignoth

#### Cargo

If the [Rust](https://www.rust-lang.org/tools/install) compiler and associated [Cargo](https://github.com/rust-lang/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](https://github.com/fxwiegand)
* [Johannes Köster](https://github.com/johanneskoester) (https://koesterlab.github.io)