Tag: Framework

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.”



[] [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: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.”


[PMID:27378302] [Bioinformatics]

Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data

“Though several tools, including genome browsers, allow such comparison at a single gene level, they do not provide a genome-wide view. We developed Heat*seq, a web-tool that allows genome scale comparison of high throughput experiments (ChIP-seq, RNA-seq and CAGE) provided by a user, to the data in the public domain. Heat*seq currently contains over 12,000 experiments across diverse tissue and cell types in human, mouse and dro-sophila. Heat*seq displays interactive correlation heatmaps, with an ability to dynamically subset datasets to contex-tualise user experiments.”