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.”

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EXaCT-1

[] [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).”

Rail-dbGaP

[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.”