FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool.
TLDR
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.Abstract:
Summary 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. Availability and implementation FQC is implemented in Python 3 and Javascript, and is maintained under an MIT license. Documentation and source code is available at: https://github.com/pnnl/fqc . Contact joseph.brown@pnnl.gov.read more
Citations
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MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis.
TL;DR: MetaWRAP is an easy-to-use modular pipeline that automates the core tasks in metagenomic analysis, while contributing significant improvements to the extraction and interpretation of high-quality metagenomics bins.
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Genome Detective: an automated system for virus identification from high-throughput sequencing data.
Michael Vilsker,Yumna Moosa,Sam Nooij,Vagner Fonseca,Vagner Fonseca,Vagner Fonseca,Yoika Ghysens,Korneel Dumon,Raf Pauwels,Luiz Carlos Junior Alcantara,Luiz Carlos Junior Alcantara,Ewout Vanden Eynden,Anne-Mieke Vandamme,Anne-Mieke Vandamme,Koen Deforche,Tulio de Oliveira +15 more
TL;DR: An easy to use web-based software application that assembles the genomes of viruses quickly and accurately using a novel alignment method that constructs genomes by reference-based linking of de novo contigs by combining amino-acids and nucleotide scores.
Journal ArticleDOI
Transcriptome and epigenome landscape of human cortical development modeled in organoids
Anahita Amiri,Gianfilippo Coppola,Soraya Scuderi,Feinan Wu,Tanmoy Roychowdhury,Fuchen Liu,Sirisha Pochareddy,Yurae Shin,Yurae Shin,Alexias Safi,Lingyun Song,Ying Zhu,André M. M. Sousa,Mark Gerstein,Gregory E. Crawford,Nenad Sestan,Alexej Abyzov,Flora M. Vaccarino +17 more
TL;DR: It is demonstrated that organoids from human pluripotent cells model cerebral cortical development on the molecular level before 16 weeks postconception, and validated hiPSC-derived cortical organoids as a suitable model system for studying gene regulation in human embryonic brain development, evolution, and disease.
Journal ArticleDOI
RNA sequencing reveals the expression profiles of circRNA and indicates that circDDX17 acts as a tumor suppressor in colorectal cancer
TL;DR: Several circRNAs that are dysregulated in CRC tissues compared with adjacent normal mucosa tissues are identified, indicating that circRNA-miRNA interactions might play important functional roles in the initiation and progression of CRC.
Journal ArticleDOI
Falco: high-speed FastQC emulation for quality control of sequencing data.
TL;DR: Falco as mentioned in this paper is an emulation of the FastQC tool that runs on average three times faster while generating equivalent results, and it also requires less memory to run and provides more flexible visualization of HTML reports.
References
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MultiQC: summarize analysis results for multiple tools and samples in a single report.
TL;DR: This work presents MultiQC, a tool to create a single report visualising output from multiple tools across many samples, enabling global trends and biases to be quickly identified.