SeqMule is an automated pipeline to generate variant calls from FASTQ or BAM files, using more than 10 popular alignment and variant calling tools.



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 have the choice to directly modify the pipeline. 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. It is developed by Yunfei Guo at Wang lab.


1. Multiple aligners

BWA-MEM, BWA-BACKTRACK, Bowtie, Bowtie2, SOAP2, 5 popular aligners are available.

2. Multiple variant callers

GATK, SAMtools, VarScan, SOAPsnp, Freebayes, 5 state-of-the-art variant callers are available. 

As stated on 1000 Genomes Project website, genotypes obtained through a consensus procedure are estimated to have 30% fewer errors than those generated by any single caller. As we have demonstrated in a previous study (O'Rawe, Jason, et al. Genome Med 5.3 [2013]: 28), consensus calls from multiple calling algorithms may increase calling accuracy and reduce Mendelian error rates.

3. Easy downloading and installation

Most jobs can be done with one-line command. Compared with most pipelines that require complicated library installation and configuration, SeqMule greatly simplifies installation. Users can do it with one command. Database preparation is also a piece of cake with one short command.

4. Fast and easy customization

Just change the 'advanced_config' file! 1 stands for enable a program and 0 for disable a program. Various parameters can be set, too. This helps users experiment with different combinations of programs or different parameters of analysis. Once a configuration file is written, you and other people can easily reproduce previous analysis.


seqmule workflow fq


Seqmule is available from


Guo Y, Lyon GJ, Wang K: SeqMule: automated human exome/genome variants detection. In submission.