This tools merges several OTU maps into one OTU map. It has an option to skip over certain prefixes that should not appear in the merged output file.


MergeOtuMaps 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 MergeOtuMaps here. To generate the usage run:

java -jar <MergeOtuMaps_jar> --help


MergeOtuMaps takes several OTU maps and merges them in a single file. You can ignore certain prefixes in the OTU maps so these entries are not included in the output file using the -p flag.


To merge two OTU maps and ignore the prefix seq8 run:

java -jar <MergeOtuMaps_jar> \
-I OtuMap1 \
-I OtuMap2 \
-o MergedOtuMaps \
-p seq8


Usage for MergeOtuMaps:

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
--input, -I yes yes (unlimited) Input OTU map. Flag needs to be specified at least 2 times: -I OTUmap1 -I OTUmap2. There is no limit to the number of OTU maps that can be merged.
--output, -o yes no Output OTU map file.
--skipPrefix, -p no yes (unlimited) Prefix that will not be included in the output file. Flag can be used multiple times.


MergeOtuMaps 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.


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

MergeOtuMaps 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 MergeOtuMaps. We have had good results with this IDE.


For any question related to MergeOtuMaps, please use the github issue tracker or contact the SASC team directly at: