This is a work in progress. The commands may change between released versions, please read the CHANGELOG.

• Goals
• Installation
• Usage
  • convert-tree
  • convert-abundance
  • combine-trees
  • combine-abundances
• Contributing
• License
• Credits

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 or from Bracken.

Binaries for Linux, OSX, and Windows are available in the Github release page. No dependencies are required.

spideog --help
spideog --version
spideog convert-tree <REPORT_FILE>
spideog convert-abundance <REPORT_FILE>
spideog combine-trees <REPORT_FILE>...
spideog combine-abundances <REPORT_FILE>...

Windows: you will need to add the .exe extension to the commands.

Convert the taxonomy tree of a Kraken report to the Newick format.

The following command will generate the file converted.tree.

spideog convert-tree sample.kreport --output converted.tree

• input: tests/sample_data/sample.kreport.
• output: tests/sample_data/converted.tree

• --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 the abundance data of a Kraken report to the CSV format.

The following command will generate the file converted.csv.

spideog convert-abundance sample.kreport --output converted.csv

• input: tests/sample_data/sample.kreport.
• output: tests/sample_data/converted.csv

• --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 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.

spideog combine-trees sample.kreport sample_2.kreport --output combined.tree

• inputs: tests/sample_data/sample.kreport and tests/sample_data/sample_2.kreport.
• output: tests/sample_data/combined.tree

• --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 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.

spideog combine-abundances sample.kreport sample_2.kreport --add-missing-taxons --output combined.csv

• inputs: tests/sample_data/sample.kreport and tests/sample_data/sample_2.kreport.
• output: tests/sample_data/combined.csv

• --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]

The project is maintained by Jean Manguy. Please submit a bug report or a feature request on the Github issues page.

spideog is distributed under the terms of both the MIT license and the Apache License (Version 2.0).

See LICENSE-APACHE and LICENSE-MIT for details.

Cover picture: Robin CC BY Greg Clarke