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.
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Mendelian disease and cancer genome analysis
Suitable for both Mendelian disease study and tumor-normal paired somatic mutation analysis
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Multiple aligners
BWA-MEM, BWA-BACKTRACK, Bowtie, Bowtie2, SOAP2, SNAP
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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.
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Easy downloading and installation.
Most jobs can be done with one-line command.
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Fast and easy customization
Just use predefined
advanced_configor change it yourself! -
Sun Grid Engine (SGE) integration
SeqMule is scalable and can utilize cluster computation resources managed by SGE.
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seqmule download: download databases/BEDs that are required by sequence alignment or variant calling software tools
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seqmule pipeline: perform the automated pipeline for detection of variants from whole-exome/genome data
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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
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seqmule run: continue run from last executed step after interruption or run from a specific step
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seqmule update: perform automated update of the SeqMule software tools See
doc/User Manual/Manualsfor details
For release history, please visit here. For details, please go here.
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.
Guo Y, Ding X, Shen Y, Lyon GJ, Wang K. SeqMule: automated human exome/genome variants detection. Scientific Reports, doi: 10.1038/srep14283, 2015
Copyright 2014-2016 USC Wang Lab