WipeReads is a tool for removing reads from indexed BAM files that are inside a user defined region. It takes pairing information into account and can be set to remove reads if one of the pairs maps outside of the target region. An application example is to remove reads mapping to known ribosomal RNA regions (using a supplied BED file containing intervals for these regions).


For documentation and manuals visit our github.io page.


WipeReads 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.


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