Welcome to the MELT homepage.

The Mobile Element Locator Tool (MELT) is a software package, written in Java, that discovers, annotates, and genotypes non-reference Mobile Element Insertions (MEIs) in Illumina DNA paired-end whole genome sequencing (WGS) data. MELT was first conceived as a tool to identify non-reference MEIs in large genome sequencing projects, specifically as part of the 1000 Genomes Project, and has been further optimized to run on a wide range of data types. MELT is optimized for performing discovery in a large number of individual sequencing samples using the Sun Grid Engine (SGE). MELT also has two additional workflows: analysis without SGE (for adaptability to other parallel computing platforms) and single genome analysis. MELT is highly scalable for many different types of data, and the different workflows are outlined and detailed in this documentation.

Please visit the downloads page to obtain a copy of MELT, and visit the Google MELT Group if you need any further assistance.

Change Log

Version 2.0.2


- added better description/explanation for the error reported in GroupAnalysis when MELT doesn’t find any hits in the IndivAnalysis step.
- Added check to the MakeVCF step to ensure all genotyping finished properly.
- Fixed error in MELT transduction finder due to unrecognized bam names.
- Fixed an error in MELT genotype where MEI masking was not working properly.

Version 2.0.1


- Added a format check for the genome annotation file (provided with -n).
- Updated some language in the help dialog provided by --help/-h.
- Several small bug fixes.
- Fixed an error in the manual that pointed to the wrong human reference file to download in the 'MELT Quick-Start Guide' section

Version 2.0.0


- Initial Release
- Several improvements beyond MELT v1.0 used for the 2015 Nature publication, see our paper for more details.