A software that accurately infers tumor purity and ploidy. It differentiates from others by performing well in low-purity and low-coverage samples.
Check Accurity for more details. Publication pending.
A software package that stratifies patients based on patient biomarker data and drug response data.
Check this page for more details.
Parallel workflow to analyze the NGS data ( Huang et al. 2015)
A workflow that analyzes ~900 monkey genomes (cumulative coverage ~4000). Starting from billions of 100bp paired-end reads by Illumina GenomeAnalyzer II, the whole workflow is comprised of several different sub-workflows: the read filtering sub-workflow (main program is a self-written java program based on GATK libraries), the read alignment sub-workflow (main program is bwa [Li et al. 2009], stampy[Lunter et al. 2011] used in test), the base-quality-score-recalibration sub-workflow by GATK [DePristo et al. 2011], the genotype-calling sub-workflow by SAMtools [Li et al. 2009] and GATK [DePristo et al. 2011], the pedigree calling sub-workflow (main program is TrioCaller [Chen et al. 2012]), and other sub-workflows that carry out the variant-filtering and statistics-calculation (Transition/Transversion, allele-frequency, mendelian inconsistency, population genetic measures such as nucleotide diversity, hardy-weinberg equilibrium p-value, linkage disequilibrium). All workflows interact with the vervet postgresql database seamlessly through sqlalchemy/elixir. The workflows were constructed in a MapReduce manner using APIs from the Pegasus workflow management system to take full advantage of the parallel computing power in most clusters. The end-result is an extremely empowering and flexible system that turns thousands of jobs into one single job, and a whole cluster into one single computer. The main code could be found at http://code.google.com/p/vervet-web/. Substantial java and C++ code are in private git repositories (available upon request).
Arabidopsis GWAS web app and database (Seren et al. 2012, Huang et al. 2011, Atwell et al. 2010)
A second-generation version is at http://gwas.gmi.oeaw.ac.at/index.html (Seren et al. 2012, source code link). The Arabidopsis polymorphism effort is at https://cynin.gmi.oeaw.ac.at/home/resources/atpolydb.