https://github.com/jeanmanguy/spideog
🐦 spideog - Command line utility for Kraken2 reports.
https://github.com/jeanmanguy/spideog
bioinformatics command-line-tool metagenomic metagenomics
Last synced: 2 months ago
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🐦 spideog - Command line utility for Kraken2 reports.
- Host: GitHub
- URL: https://github.com/jeanmanguy/spideog
- Owner: jeanmanguy
- License: apache-2.0
- Created: 2020-10-07T14:37:17.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2020-11-30T11:39:15.000Z (almost 5 years ago)
- Last Synced: 2025-06-21T17:18:13.298Z (4 months ago)
- Topics: bioinformatics, command-line-tool, metagenomic, metagenomics
- Language: Rust
- Homepage:
- Size: 88.9 KB
- Stars: 12
- Watchers: 1
- Forks: 1
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE-APACHE
Awesome Lists containing this project
README
# 🐦 spideog - Command line utility for Kraken2 reports.
[](https://github.com/jeanmanguy/spideog/releases/tag/v0.1.2-alpha.1)
[](https://travis-ci.com/jeanmanguy/spideog)
[](https://github.com/jeanmanguy/spideog/actions?query=workflow%3ARust)
This is a work in progress. The commands may change between released versions, please read the [CHANGELOG](CHANGELOG).
- [Goals](#goals)
- [Installation](#installation)
- [Usage](#usage)
- [`convert-tree`](#convert-tree)
- [`convert-abundance`](#convert-abundance)
- [`combine-trees`](#combine-trees)
- [`combine-abundances`](#combine-abundances)
- [Contributing](#contributing)
- [License](#license)
- [Credits](#credits)
## Goals
The first goal of this project is to convert Kraken reports into standard file formats that can be easily read with R to allow people to craft thier own data visualisations and compute statistics more easily using the tidyverse, vegan, ape, and ggtree/treeio. The second goal is to get summary information from the Kraken reports directly from the command line.
Supports Kraken reports from [Kraken2](https://github.com/DerrickWood/kraken2) or from [Bracken](https://github.com/jenniferlu717/Bracken).
## Installation
Binaries for Linux, OSX, and Windows are available in the [Github release page](https://github.com/jeanmanguy/spideog/releases). No dependencies are required.
## Usage
```sh
spideog --help
spideog --version
spideog convert-tree
spideog convert-abundance
spideog combine-trees ...
spideog combine-abundances ...
```
Windows: you will need to add the `.exe` extension to the commands.
### `convert-tree`
Convert the taxonomy tree of a Kraken report to the Newick format.
The following command will generate the file `converted.tree`.
```sh
spideog convert-tree sample.kreport --output converted.tree
```
### Example files
- input: [tests/sample_data/sample.kreport](tests/sample_data/sample.kreport).
- output: [tests/sample_data/converted.tree](tests/sample_data/converted.tree)
#### Options
- `--has-headers` necessary if the input report has headers
- `--output` output file path
- `--overwrite` force overwriting if the output file already exist
- `--report-format` input format (default: Kraken) [Only Kraken reports are supported at the moment]
- `--format` output format (default: newick) [Only newick is supported at the moment]
### `convert-abundance`
Convert the abundance data of a Kraken report to the CSV format.
The following command will generate the file `converted.csv`.
```sh
spideog convert-abundance sample.kreport --output converted.csv
```
### Example files
- input: [tests/sample_data/sample.kreport](tests/sample_data/sample.kreport).
- output: [tests/sample_data/converted.csv](tests/sample_data/converted.csv)
#### Options
- `--has-headers` necessary if the input report has headers
- `--output` output file path
- `--overwrite` force overwriting if the output file already exist
- `--report-format` input format (default: Kraken) [Only Kraken reports are supported at the moment]
- `--format` output format (default: CSV) [Only CSV is supported at the moment]
### `combine-trees`
Combine and convert taxonomy trees from multiple Kraken report (e.g. from different samples of the same experiment) to the Newick format.
The following command will generate the file `combined.tree`.
```sh
spideog combine-trees sample.kreport sample_2.kreport --output combined.tree
```
### Example files
- inputs: [tests/sample_data/sample.kreport](tests/sample_data/sample.kreport) and [tests/sample_data/sample_2.kreport](tests/sample_data/sample_2.kreport).
- output: [tests/sample_data/combined.tree](tests/sample_data/combined.tree)
#### Options
- `--has-headers` necessary if the input reports have headers
- `--output` output file path
- `--overwrite` force overwriting if the output file already exist
- `--report-format` input format (default: Kraken) [Only Kraken reports are supported at the moment]
- `--format` output format (default: newick) [Only newick is supported at the moment]
### `combine-abundances`
Combine and convert abundance data from multiple Kraken report (e.g. from different samples of the same experiment) to the CSV format.
The following command will generate the file `combined.csv`.
```sh
spideog combine-abundances sample.kreport sample_2.kreport --add-missing-taxons --output combined.csv
```
### Example files
- inputs: [tests/sample_data/sample.kreport](tests/sample_data/sample.kreport) and [tests/sample_data/sample_2.kreport](tests/sample_data/sample_2.kreport).
- output: [tests/sample_data/combined.csv](tests/sample_data/combined.csv)
#### Options
- `--add-missing-taxons` add missig taxons in some reports but present in other with zero values
- `--has-headers` necessary if the input report has headers
- `--output` output file path
- `--overwrite` force overwriting if the output file already exist
- `--report-format` input format (default: Kraken) [Only Kraken reports are supported at the moment]
- `--format` output format (default: CSV) [Only CSV is supported at the moment]
## Contributing
The project is maintained by Jean Manguy. Please submit a bug report or a feature request [on the Github issues page](https://github.com/jeanmanguy/spideog/issues/new/choose).
## License
`spideog` is distributed under the terms of both the MIT license and the
Apache License (Version 2.0).
See [LICENSE-APACHE](./LICENSE-APACHE) and [LICENSE-MIT](./LICENSE-MIT) for
details.
## Credits
Cover picture: [Robin CC BY Greg Clarke](https://www.flickr.com/photos/leppre/25468458218)