skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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. Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA and
  2. Computation and Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA
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 Name: Bioinformatics Journal Volume: 33 Journal Issue: 19; Journal ID: ISSN 1367-4803
Publisher:
Oxford University Press
Country of Publication:
United Kingdom
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 59 BASIC BIOLOGICAL SCIENCES; data and text mining

Citation Formats

Brown, Joseph, Pirrung, Meg, McCue, Lee Ann, and Wren, ed., Jonathan. FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. United Kingdom: N. p., 2017. Web. doi:10.1093/bioinformatics/btx373.
Brown, Joseph, Pirrung, Meg, McCue, Lee Ann, & Wren, ed., Jonathan. FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. United Kingdom. doi:https://doi.org/10.1093/bioinformatics/btx373
Brown, Joseph, Pirrung, Meg, McCue, Lee Ann, and Wren, ed., Jonathan. Fri . "FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool". United Kingdom. doi:https://doi.org/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 and Wren, ed., Jonathan},
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 Kingdom},
year = {2017},
month = {6}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: https://doi.org/10.1093/bioinformatics/btx373

Citation Metrics:
Cited by: 77 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

Save / Share:

Works referencing / citing this record:

Characterization of genes required for both Rpg1 and rpg4-mediated wheat stem rust resistance in barley
journal, June 2019


Heterozygous diploid structure of Amorphotheca resinae ZN1 contributes efficient biodetoxification on solid pretreated corn stover
journal, May 2019


Involvement of Salicylic Acid in Anthracnose Infection in Tea Plants Revealed by Transcriptome Profiling
journal, May 2019

  • Shi, Yun-Long; Sheng, Yue-Yue; Cai, Zhuo-Yu
  • International Journal of Molecular Sciences, Vol. 20, Issue 10
  • DOI: 10.3390/ijms20102439

Characterization of genes required for both Rpg1 and rpg4-mediated wheat stem rust resistance in barley
journal, June 2019


Heterozygous diploid structure of Amorphotheca resinae ZN1 contributes efficient biodetoxification on solid pretreated corn stover
journal, May 2019


Involvement of Salicylic Acid in Anthracnose Infection in Tea Plants Revealed by Transcriptome Profiling
journal, May 2019

  • Shi, Yun-Long; Sheng, Yue-Yue; Cai, Zhuo-Yu
  • International Journal of Molecular Sciences, Vol. 20, Issue 10
  • DOI: 10.3390/ijms20102439

Comprehensive analysis of long noncoding RNA and mRNA in five colorectal cancer tissues and five normal tissues
journal, February 2020

  • Zhou, Zhen-Xu; Chen, Xiao-Ming; Zhang, Yu-Qi
  • Bioscience Reports, Vol. 40, Issue 2
  • DOI: 10.1042/bsr20191139

D evelopmental C hromatin R estriction of P ro‐ G rowth G ene N etworks A cts as an E pigenetic B arrier to A xon R egeneration in C ortical N eurons
journal, June 2018

  • Venkatesh, Ishwariya; Mehra, Vatsal; Wang, Zimei
  • Developmental Neurobiology, Vol. 78, Issue 10
  • DOI: 10.1002/dneu.22605

Gene expression in retinal ischemic post-conditioning
journal, March 2018

  • Kadzielawa, Konrad; Mathew, Biji; Stelman, Clara R.
  • Graefe's Archive for Clinical and Experimental Ophthalmology, Vol. 256, Issue 5
  • DOI: 10.1007/s00417-018-3905-0

Klotho Is Neuroprotective in the Superoxide Dismutase (SOD1G93A) Mouse Model of ALS
journal, June 2019


Inter-Kingdom beach warfare: Microbial chemical communication activates natural chemical defences
journal, August 2018

  • Khalil, Zeinab G.; Cruz-Morales, Pablo; Licona-Cassani, Cuauhtemoc
  • The ISME Journal, Vol. 13, Issue 1
  • DOI: 10.1038/s41396-018-0265-z

An optimized chemical-genetic method for cell-specific metabolic labeling of RNA
journal, February 2020


Transcriptomic profiling of cotton Gossypium hirsutum challenged with low-temperature gradients stress
journal, October 2019


KLF6 and STAT3 co-occupy regulatory DNA and functionally synergize to promote axon growth in CNS neurons
journal, August 2018


Reaction parameter comparison and optimization of multiple displacement amplification
journal, January 2020

  • Huang, Mengting; Yang, Fang; Fu, Jiye
  • Analytical Methods, Vol. 12, Issue 1
  • DOI: 10.1039/c9ay01922g

Genome Detective: an automated system for virus identification from high-throughput sequencing data
journal, August 2018


Interplay between small RNA pathways shapes chromatin landscapes in C. elegans
journal, April 2019

  • Gushchanskaia, Ekaterina S.; Esse, Ruben; Ma, Qicheng
  • Nucleic Acids Research, Vol. 47, Issue 11
  • DOI: 10.1093/nar/gkz275

Gross transcriptomic analysis of Pseudomonas putida for diagnosing environmental shifts
journal, January 2020

  • Hueso‐Gil, Ángeles; Calles, Belén; O'Toole, George A.
  • Microbial Biotechnology, Vol. 13, Issue 1
  • DOI: 10.1111/1751-7915.13404

Oncostatin M inhibits differentiation of rat stem Leydig cells in vivo and in vitro
journal, October 2018

  • Wang, Yiyan; Xie, Lubin; Tian, Erpo
  • Journal of Cellular and Molecular Medicine, Vol. 23, Issue 1
  • DOI: 10.1111/jcmm.13946

Fibroblast growth factor homologous factor 1 stimulates Leydig cell regeneration from stem cells in male rats
journal, June 2019

  • Mo, Jiaying; Chen, Xiuxiu; Ni, Chaobo
  • Journal of Cellular and Molecular Medicine, Vol. 23, Issue 8
  • DOI: 10.1111/jcmm.14461

Kinetics of hepatitis B surface antigen quasispecies during REP 2139‐Ca therapy in HBeAg‐positive chronic HBV infection
journal, August 2019

  • Usman, Zainab; Mijočević, Hrvoje; Karimzadeh, Hadi
  • Journal of Viral Hepatitis, Vol. 26, Issue 12
  • DOI: 10.1111/jvh.13180

Ethylene‐responsive factor 4 is associated with the desirable rind hardness trait conferring cracking resistance in fresh fruits of watermelon
journal, October 2019

  • Liao, Nanqiao; Hu, Zhongyuan; Li, Yingying
  • Plant Biotechnology Journal, Vol. 18, Issue 4
  • DOI: 10.1111/pbi.13276

Transcriptome and epigenome landscape of human cortical development modeled in organoids
journal, December 2018


Antibiotics and Host-Tailored Probiotics Similarly Modulate Effects on the Developing Avian Microbiome, Mycobiome, and Host Gene Expression
journal, October 2019

  • Ward, Tonya L.; Weber, Bonnie P.; Mendoza, Kristelle M.
  • mBio, Vol. 10, Issue 5
  • DOI: 10.1128/mbio.02171-19

VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites
journal, November 2017


Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity
journal, February 2020

  • Hendriks, Amber C. A.; Reubsaet, Frans A. G.; Kooistra-Smid, A. M. D. ( Mirjam)
  • BMC Genomics, Vol. 21, Issue 1
  • DOI: 10.1186/s12864-020-6555-7

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
journal, September 2018


Ancestry patterns inferred from massive RNA-seq data
journal, April 2019


Falco: high-speed FastQC emulation for quality control of sequencing data
journal, January 2019


A Microglial Signature Directing Human Aging and Neurodegeneration-Related Gene Networks
journal, January 2019

  • Mukherjee, Shradha; Klaus, Christine; Pricop-Jeckstadt, Mihaela
  • Frontiers in Neuroscience, Vol. 13
  • DOI: 10.3389/fnins.2019.00002

Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome
journal, March 2019


Methionine Adenosyltransferase 1a (MAT1A) Enhances Cell Survival During Chemotherapy Treatment and is Associated with Drug Resistance in Bladder Cancer PDX Mice
journal, October 2019

  • Martin, Kelly A.; Hum, Nicholas R.; Sebastian, Aimy
  • International Journal of Molecular Sciences, Vol. 20, Issue 20
  • DOI: 10.3390/ijms20204983

    Figures / Tables found in this record:

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