Description

This tool converts the Kraken-report output into a JSON format. The tool can output to file or stdout. This allows the report to be used in pipelines.

Installation

KrakenReportToJson requires Java 8 to be installed on your device. Download Java 8 here or install via your distribution's package manager.

Download the latest version of KrakenReportToJson here. To generate the usage run:

java -jar <KrakenReportToJson_jar> --help

Manual

KrakenReportToJson can write to an output file or stdout. It can optionally not include the scientific names in the output if the --skipnames flag is used.

Example

To convert a krakenreport to a json on stdout:

java -jar <KrakenReportToJson_jar> \
-i krakenreport

To convert a krakenreport to an output file and skip the scientific names:

java -jar <KrakenReportToJson_jar> \
-i krakenreport \
-o krakenreport.json \
--skipnames=true

Usage

Usage for KrakenReportToJson:

Option	Required	Can occur multiple times	Description
--log_level, -l	no	no	Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error'
--help, -h	no	no	Print usage
--version, -v	no	no	Print version
--krakenreport, -i	yes	no	Kraken report to generate stats from
--output, -o	no	no	File to write output to, if not supplied output go to stdout
--skipnames, -n	no	no	Don't report the scientific name of the taxon.

About

KrakenReportToJson is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of a pipeline, for example the SASC team's biowdl pipelines.

All tools in the BIOPET tool suite are Free/Libre and Open Source Software.

Contributing

The source code of KrakenReportToJson can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.

KrakenReportToJson is build using sbt. Before submitting a pull request, make sure all tests can be passed by running sbt test from the project's root. We recommend using an IDE to work on KrakenReportToJson. We have had good results with this IDE.

Contact

For any question related to KrakenReportToJson, please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.