FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool

Brown, Joseph; Pirrung, Meg; McCue, Lee Ann

doi:10.1093/BIOINFORMATICS/BTX373

Title: FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool

Journal Article · 09 June 2017 · Bioinformatics

DOI: https://doi.org/10.1093/BIOINFORMATICS/BTX373 · OSTI ID:1460473

Brown, Joseph ^[1]; Pirrung, Meg ^[2]; McCue, Lee Ann ^[1]

Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Earth and Biological Sciences Division
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Computation and Analytics Division

FQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly summarize individual sequencing runs. The dashboard groups samples in dropdowns for navigation among the data sets, utilizes human-readable configuration files to manipulate the pages and tabs, and is extensible with CSV data.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE; PNNL Laboratory Directed Research and Development (LDRD) Program

Grant/Contract Number:: AC06-76RL01830

OSTI ID:: 1460473

Alternate ID(s):: OSTI ID: 1430724

Report Number(s):: PNNL-SA-124428

Journal Information:: Bioinformatics, Vol. 33, Issue 19; ISSN 1367-4803

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 401 works

Citation information provided by
Web of Science

References (1)

MultiQC: summarize analysis results for multiple tools and samples in a single report Ewels, Philip; Magnusson, Måns; Lundin, Sverker Bioinformatics, Vol. 32, Issue 19 https://doi.org/10.1093/bioinformatics/btw354	journal	June 2016

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