Tag: Framework

Workflow for WGS CNV

[PMID: 29304372] [American Journal of Human Genetics]

A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data

“Here, we used several datasets to empirically develop a detailed workflow for identifying germline CNVs >1 kb from short-read WGS data using read depth-based algorithms.”



[PMID: 28911107] [Nucleic Acids Research]

Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs

“provides a wide range of modules for quantification of miRNAs and other non-coding RNAs, discovering new miRNAs, isomiRs, mutations, exogenous RNAs and motifs. Use-cases comprising hundreds of samples are processed in less than 5 h with an accuracy of 99.4%.”


[PMID: 28522612] [Genome Research]

GenomeVIP: a cloud platform for genomic variant discovery and interpretation

“an open-source framework for performing genomics variant discovery and annotation using cloud- or local high-performance computing infrastructure.” Work from Li Ding.



[PMID: 28750683] [Genome Biology]

Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network

“to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation changes in the DNase I hypersensitivity based regulatory network. “



[PMID: 28669402] [American Journal of Human Genetics]

SEQSpark: A Complete Analysis Tool for Large-Scale Rare Variant Association Studies using Whole-Genome and Exome Sequence Data

“implements parallel processing based on Spark to increase the speed and efficiency of performing data quality control, annotation, and association analysis.”



[PMID:28492532] [Genetics in Medicine]

Sherloc: a comprehensive refinement of the ACMG–AMP variant classification criteria

“Sherloc (semiquantitative, hierarchical evidence-based rules for locus interpretation), a variant classification framework that is an effective refinement of the ACMG–AMP criteria.”



[PMID:28426665] [PLoS Computational Biology]

Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples

“a new ‘domain-centric’ method for identifying clusters of somatic mutations across entire gene families using protein domain models.”