Genomon-exome Overview
Genomon-exome is pipeline software comprising a suite of bioinformatics tools and optimally designed for exome sequencing data analysis. In the pipeline, users can map exome sequenced reads from fastq files against the hg19 human genome reference and realign the mapped reads to obtain a list of mutation candidates. This pipeline software is freely available, modifiable and redistributed under the License. Currently, the pipeline assumes that the exome sequenced data are from human and the hg19 human genome reference is used throughout the pipeline workflow.
| Genomon-exome is a collaborative effort between the laboratories: |
| Miyano Laboratory, Human Genome Center, The Institute of Medical Science, The University of Tokyo. |
| Ogawa Laboratory, Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University. |
Genomon-exome needs to be used on the supercomputer at Human Genome Center, and this software is freely available, modifiable and redistributed under the Genomon License. Please refer to the License before using this software.
The entire source code is provided at the GitHub, https://github.com/Genomon. For installation instructions, please refer to the INSTALL page.
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Frequent pathway mutations of splicing machinery in myelodysplasia. Nature 478, 64-69 (06 October 2011) |
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ACTN1 Mutations Cause Congenital Macrothrombocytopenia. The American Journal of Human Genetics 92, 1-8, March 7, 2013 |
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An empirical Bayesian framework for mutation detection from cancer genome sequencing data. Nucleic Acids Research (First published online: March 6, 2013) |
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Integrated molecular analysis of clear-cell renal cell carcinoma. Nature Genetics (Published online: 24 June 2013) |
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Somatic SETBP1 mutations in myeloid malignancies. Nature Genetics (Published online: 07 July 2013) |
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Exome sequencing identifies secondary mutations of SETBP1 and JAK3 in juvenile myelomonocytic leukemia. Nature Genetics (Published online: 07 July 2013) |
Genomon-exome is a pipeline that does mapping and analyze data.
Features
Below are the features of the Genomon-exome pipeline software.
- cutadapt is used to remove PCR artifacts (adapter sequences).
- BWA(Burrows-Wheeler Aligner) is used to map short-reads from fastq files against the hg19 human reference.
- GATK(The Genome Analysis Toolkit) is used to realign bam files.
- Picard is used to obtain alignment information such as about mapping rates and coverages.
- Mutation candidates come in the form of .tsv files.
- ANNOVAR is used to annotate possible mutation candidates.
- Averaged regions copy number can be detected.
- This pipeline software is designed to be used on the supercomputer at Human Genome Center.
- One sample is analyzed within a day. Maximally 10 samples can be analyzed simultaneously, but this is subject to the computing resource you can use.
Acknowledgements
This work has been supported by MEXT Grant-in-Aid Scientific Research on Innovative Areas, grant No. 4201 (Systems Cancer Project - Integrative Systems Understanding of Cancer for Advanced Diagnosis, Therapy and Prevention -) .
Genomon-exome uses the packages below: