This tool rebuilds a contig map, so the contig names used are equal to those in a given fasta reference.


RebuildContigMap 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 RebuildContigMap here. To generate the usage run:

java -jar <RebuildContigMap_jar> --help


RebuildContigMap requires the original contig map and a reference fasta file. It will then reconstruct the contig map and output it at the given path. Contig maps should be in tsv format.


To construct a new contig map with contig names that match the fasta reference:

java -jar <RebuildContigMap_jar> \
-I oldContigMap.tsv \
-R reference.fasta \
-o newContigMap.tsv


Usage for RebuildContigMap:

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
--inputContigMap, -I yes no Input contig map
--outputContigMap, -o yes no output contig map
--referenceFasta, -R yes no Reference fasta file


RebuildContigMap 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 RebuildContigMap can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.

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


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