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seqmule website  

SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file. SeqMule also has some built-in functions, such as pooling consensus calls from various callers, plotting a Venn diagram showing intersection among different callers, and downloading databases. SeqMule can be used for both Mendelian disease study and cancer genome study.

Environment Modules

Run module spider seqmule to find out what environment modules are available for this application.

System Variables

  • HPC_SEQMULE_DIR - installation directory
  • HPC_SEQMULE_BIN - executable directory


If you publish research that uses seqmule you have to cite it as follows:

Guo Y, Ding X, Shen Y, Lyon GJ, Wang K. SeqMule: automated human exome/genome variants detection. Scientific Reports, doi: 10.1038/srep14283, 2015