Squishbed makes a BED file smaller by removing bases that are in overlapping records. Squishbed will report the number of bases before and after squishing.


For documentation and manuals visit our github.io page.


SquishBed 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 SquishBed, please use the github issue tracker or contact the SASC team directly at: [email protected].