Tag: Framework

SEQSpark

[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.”

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Sherloc

[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.”

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.”

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).”