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

Brown, James C.; Pirrung, Megan; McCue, Lee Ann

doi:10.1093/bioinformatics/btx373

Cited by 648 publications

(446 citation statements)

References 1 publication

(1 reference statement)

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“…Read pairs with a read mean quality score below 30 or a read length shorter than 75 of the read length (i.e.,105bp) were also discarded. FastQCv0.11.7 [17] was performed on the remaining reads (Pass Filter Reads). Paired-end FASTQ files were separately merged in case of multiple read files for the same sample.…”

Section: Methodsmentioning

confidence: 99%

Spike-in Genomic DNA for Validating Performance of Metagenomics Workflows

Venkataraman

Parlov

et al. 2018

BioTechniques

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Shotgun metagenomics is a powerful platform to characterize human microbiomes. However, to translate such survey data into consumer-relevant products or services, it is critical to have a robust metagenomics workflow. We present a tool - spike-in DNA - to assess performance of metagenomics workflows. The spike-in is DNA from two organisms - Alivibrio fischeri and Rhodopseudomonas palustris, in a ratio of 4:1 added to samples before DNA extraction. With a valid workflow, the output ratio of relative abundances of these organisms should be close to 4. This expectation was tested in samples of varying diversities (n = 110), and the mean ratio was 4.73 (99% CI [4.0, 5.24]). We anticipate this tool to be a relevant community resource for assessing the quality of shotgun metagenomics workflows and thereby enable robust characterization of microbiomes.

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Section: Methodsmentioning

confidence: 99%

Spike-in Genomic DNA for Validating Performance of Metagenomics Workflows

Venkataraman

Parlov

et al. 2018

BioTechniques

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“…3'prime mRNA-seq libraries containing unique molecular identifiers (UMIs) were prepared De-multiplexed FASTQ files were inspected for quality using FASTQC (Brown et al, 2017). Reads were aligned to GRCh38 using the STAR two-pass method (Dobin et al, 2013).…”

Section: Mrna-seq Library Preparation and Data Pre-processingmentioning

confidence: 99%

WNT and inflammatory signaling distinguish human Fallopian tube epithelial cell populations

Rose

Bidarimath

Webster

et al. 2020

Preprint

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A substantial fraction of ovarian/extra-uterine high-grade serous carcinomas (HGSCs) likely originate in the distal region of the Fallopian tube's epithelium (TE) before implanting/metastasizing to the ovary. Unfortunately, molecular and cellular mechanisms rendering preferential cancer susceptibility of the human distal TE remain insufficiently elucidated, largely due to limited primary human TE gene expression data. Here we report an in depth bioinformatic characterization of 34 primary TE cell mRNA-seq samples.These samples were prepared from the proximal and distal TE regions of 12 normal Fallopian tubes. TE cells were segregated based on their aldehyde dehydrogenase (ALDH) activity. As compared to the proximal TE, cells from the distal region form organoids with higher frequency and larger size during serial organoid formation assays. Consistent with enrichment for organoid-forming stem/progenitor cells, ALDH+ cells have greater WNT signaling activity. Comparative evaluation of proximal and distal TE cell population's shows heightened inflammatory signaling in distal differentiated (ALDH-) TE.Furthermore, comparisons of proximal and distal TE cell populations finds that the distal TE express gene sets characteristic of four HGSC molecular sub-types, and that distal ALDH+ cell populations exhibit greater enrichment than their ALDH-counterparts. Taken together, our study shows that increased organoid forming capacity, WNT and inflammatory signaling, and HGSC signatures underlie the differences between distal and proximal regions of the human TE. These findings provide the basis for further mechanistic studies of distal TE susceptibility to the malignant transformation.

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“…We obtained an average of 180.9 billion total raw bases per sample (range 117.81 to 523.49 billion bases). The quality of raw fastq files was assessed using FASTQC (Brown et al, 2017). Reads were then aligned to the human b37 genome assembly with decoy sequences included and a Sendai virus contig with the BWA-mem algorithm under default parameters .…”

Section: Discussionmentioning

confidence: 99%

Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats

Jakubosky

Smith

D’Antonio

et al. 2019

Preprint

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Structural variants (SVs) and short tandem repeats (STRs) are important sources of genetic diversity but are not routinely analyzed in genetic studies because they are difficult to accurately identify and genotype. Because SVs and STRs range in size and type, it is necessary to apply multiple algorithms that incorporate different types of evidence from sequencing data and employ complex filtering strategies to discover a comprehensive set of high-quality and reproducible variants. Here we assembled a set of 719 deep whole genome sequencing (WGS) samples (mean 42x) from 477 distinct individuals which we used to discover and genotype a wide spectrum of SV and STR variants using five algorithms. We used 177 unique pairs of genetic replicates to identify factors that affect variant call reproducibility and developed a systematic filtering strategy to create of one of the most complete and well characterized maps of SVs and STRs to date.

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

Cited by 648 publications

References 1 publication

Spike-in Genomic DNA for Validating Performance of Metagenomics Workflows

Spike-in Genomic DNA for Validating Performance of Metagenomics Workflows

WNT and inflammatory signaling distinguish human Fallopian tube epithelial cell populations

Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats

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