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

Abstract

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.

Authors:
 [1];  [2];  [1]
  1. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Earth and Biological Sciences Division
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Computation and Analytics Division
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE; PNNL Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
1460473
Alternate Identifier(s):
OSTI ID: 1430724
Report Number(s):
PNNL-SA-124428
Journal ID: ISSN 1367-4803
Grant/Contract Number:  
AC06-76RL01830
Resource Type:
Published Article
Journal Name:
Bioinformatics
Additional Journal Information:
Journal Volume: 33; Journal Issue: 19; Journal ID: ISSN 1367-4803
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 59 BASIC BIOLOGICAL SCIENCES; data and text mining

Citation Formats

Brown, Joseph, Pirrung, Meg, and McCue, Lee Ann. FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. United States: N. p., 2017. Web. doi:10.1093/BIOINFORMATICS/BTX373.
Brown, Joseph, Pirrung, Meg, & McCue, Lee Ann. FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. United States. doi:10.1093/BIOINFORMATICS/BTX373.
Brown, Joseph, Pirrung, Meg, and McCue, Lee Ann. Fri . "FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool". United States. doi:10.1093/BIOINFORMATICS/BTX373.
@article{osti_1460473,
title = {FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool},
author = {Brown, Joseph and Pirrung, Meg and McCue, Lee Ann},
abstractNote = {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.},
doi = {10.1093/BIOINFORMATICS/BTX373},
journal = {Bioinformatics},
number = 19,
volume = 33,
place = {United States},
year = {2017},
month = {6}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1093/BIOINFORMATICS/BTX373

Citation Metrics:
Cited by: 35 works
Citation information provided by
Web of Science

Figures / Tables:

Fig. 1 Fig. 1: The FQC dashboard. (A) Tab navigation with the metric name displayed on the tab and status of the metric as determined by FastQC. (B) Dropdown menus of the groups (in this example, a group represents a flow cell) and biological samples within a group available for viewing. (C)more » Plot tabs enable switching between multiple plots (R1 and R2 reads in this example) within a given quality metric. (D) 96-well reagent plate heatmap with positive controls encircled in red; this example shows positive control sample bleed-over into neighboring plate wells. (E) Read abundance values across a reagent plate showing potential dispensing robot failure after column 8. (F) A Lorenz curve showing the distribution of on-target reads across sequence barcodes. A live FQC example site is available at: https://pnnl.github.io/fqc/« less

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Works referenced in this record:

MultiQC: summarize analysis results for multiple tools and samples in a single report
journal, June 2016


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      Figures / Tables found in this record:

        Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.