Tag: Framework

Reproducible Computational Workflows

[PMID:28288103] [Nature Biotechnology]

Reproducibility of computational workflows is automated using continuous analysis

“We report the development of continuous analysis, a workflow that enables reproducible computational analyses. Continuous analysis combines Docker, a container technology akin to virtual machines, with continuous integration, a software development technique, to automatically rerun a computational analysis whenever updates or improvements are made to source code or data.”

[PMID:28398311] [Nature Biotechnology]

Nextflow enables reproducible computational workflows

“Nextflow, a workflow management system that uses Docker technology for the multi-scale handling of containerized computation.”


MPEG HTS Compression Working Group

[PMID:27776113] [Nature Methods]

Comparison of high-throughput sequencing data compression tools

“to evaluate all available approaches used for HTS data compression. These approaches include both industry-scale tools as well as research-oriented prototypes. Compression performance, running times, memory usage and parallelization capabilities were measured for each tool.”

Small RNA-Seq Workflow

[PMID: 27317696] [Nucleic Acids Research]

Toward reliable biomarker signatures in the age of liquid biopsies – how to standardize the small RNA-Seq workflow



[] [Genomic Medicine]

Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care

“…whole-exome sequencing (WES)-based test for precision cancer care. EXaCT-1 uses HaloPlex (Agilent) target enrichment followed by next-generation sequencing (Illumina) of tumour and matched constitutional control DNA. ” “uitable for simultaneous detection of somatic point/indel mutations and copy-number alterations (CNAs).”



[PMID:27311963] [Genome Biology]

OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations

“a method designed to analyze the pattern of somatic mutations across tumors in both coding and non-coding genomic regions to identify signals of positive selection, and therefore, their involvement in tumorigenesis.”



[PMID:27187206] [Bioinformatics]

SoFIA: a data integration framework for annotating high-throughput datasets

“a framework for workflow-driven data integration with a focus on genomic annotation.”



[PMID:27153614] [Bioinformatics]

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce

Work from Ben Langmead. “To analyse dbGaP-protected data, researchers must typically work with IT administrators and signing officials to ensure all levels of security are implemented at their institution. This is a major obstacle, impeding reproducibility and reducing the utility of archived data.” “The protocol, Rail-dbGaP, is applicable to any tool running on Amazon Web Services Elastic MapReduce.”