SeqMule: Automated human exome/genome variants detection

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.

Features

Mendelian disease and cancer genome analysis

Suitable for both Mendelian disease study and tumor-normal paired somatic mutation analysis
Multiple aligners

BWA-MEM, BWA-BACKTRACK, Bowtie, Bowtie2, SOAP2, SNAP
Multiple variant callers

GATK, SAMtools, VarScan, SOAPsnp, Freebayes 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 et al. Genome Med 2013, 5:28), consensus calls from multiple calling algorithms may increase calling accuracy and reduce Mendelian error rates.
Easy downloading and installation.

Most jobs can be done with one-line command.
Fast and easy customization

Just use predefined advanced_config or change it yourself!
Sun Grid Engine (SGE) integration

SeqMule is scalable and can utilize cluster computation resources managed by SGE.

Synopsis

seqmule download: download databases/BEDs that are required by sequence alignment or variant calling software tools
seqmule pipeline: perform the automated pipeline for detection of variants from whole-exome/genome data
seqmule stats: perform statistical analysis of variants data, such as drawing Venn diagram to examine overlap between VCF files, generating union/consensus ca lls, generating coverage/alignment statistics in specific genomic regions, calculating Mendelian error rates
seqmule run: continue run from last executed step after interruption or run from a specific step
seqmule update: perform automated update of the SeqMule software tools See doc/User Manual/Manuals for details

Revision History

For release history, please visit here. For details, please go here.

Contact

For questions/bugs/issues, please post on GitHub. In general, please do NOT send questions to our email. Your question may be very likely to help other users.

Please join SeqMule-dev for updates.

Citation

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