https://github.com/wglab/seqmule
Automated human exome/genome variants detection from FASTQ files
https://github.com/wglab/seqmule
Last synced: 6 months ago
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Automated human exome/genome variants detection from FASTQ files
- Host: GitHub
- URL: https://github.com/wglab/seqmule
- Owner: WGLab
- License: other
- Created: 2014-05-29T20:39:30.000Z (about 12 years ago)
- Default Branch: master
- Last Pushed: 2021-09-27T12:39:36.000Z (almost 5 years ago)
- Last Synced: 2026-01-14T01:53:44.253Z (6 months ago)
- Language: C++
- Homepage: http://seqmule.usc.edu
- Size: 24.9 MB
- Stars: 23
- Watchers: 13
- Forks: 23
- Open Issues: 48
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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**
## Docker image
https://hub.docker.com/repository/docker/genomicslab/seqmule
## Revision History
For release history, please visit [here](https://github.com/WGLab/SeqMule/releases). For details, please go [here](https://github.com/WangGenomicsLab/SeqMule/commits/master).
## Contact
For questions/bugs/issues, please post on [GitHub](https://github.com/WGLab/SeqMule/issues). In general, please do NOT send questions to our email. Your question may be very likely to help other users.
Please join [SeqMule-dev](https://groups.google.com/forum/#!forum/seqmule-dev) for updates.
## Citation
Guo Y, Ding X, Shen Y, Lyon GJ, Wang K. [SeqMule: automated human exome/genome variants detection](http://www.nature.com/articles/srep14283). Scientific Reports, doi: 10.1038/srep14283, 2015
## More information
* [SeqMule Homepage](http://seqmule.openbioinformatics.org)
* [Wang Genomics Lab Homepage](http://wglab.org)
Copyright 2014-2021 [USC Wang Lab](http://wglab.org)