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Bioinformatics (Oxford, England) Sep 2018Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each...
MOTIVATION
Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient.
RESULTS
We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2-5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools.
AVAILABILITY AND IMPLEMENTATION
The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.
Topics: Humans; Programming Languages; Quality Control
PubMed: 30423086
DOI: 10.1093/bioinformatics/bty560 -
F1000Research 2018DNA sequencing analysis typically involves mapping reads to just one reference genome. Mapping against multiple genomes is necessary, however, when the genome of origin...
DNA sequencing analysis typically involves mapping reads to just one reference genome. Mapping against multiple genomes is necessary, however, when the genome of origin requires confirmation. Mapping against multiple genomes is also advisable for detecting contamination or for identifying sample swaps which, if left undetected, may lead to incorrect experimental conclusions. Consequently, we present FastQ Screen, a tool to validate the origin of DNA samples by quantifying the proportion of reads that map to a panel of reference genomes. FastQ Screen is intended to be used routinely as a quality control measure and for analysing samples in which the origin of the DNA is uncertain or has multiple sources.
Topics: Chromosome Mapping; Genome; High-Throughput Nucleotide Sequencing; Quality Control; Sequence Analysis, DNA; Software
PubMed: 30254741
DOI: 10.12688/f1000research.15931.2 -
Molecular Cell Apr 2022
Topics: Quality Control
PubMed: 35452607
DOI: 10.1016/j.molcel.2022.04.004 -
Current Opinion in Structural Biology Aug 2021Membrane proteins account for a quarter of cellular proteins, and most are synthesised at the endoplasmic reticulum (ER). Insertion and folding of polypeptides in the... (Review)
Review
Membrane proteins account for a quarter of cellular proteins, and most are synthesised at the endoplasmic reticulum (ER). Insertion and folding of polypeptides in the membrane environment is prone to error, necessitating diverse quality control systems. Recent discoveries have demonstrated how forces act on the nascent chain during insertion, and revealed new translocon components and accessories that facilitate the correct biogenesis of substrates. Our understanding of one of the best studied quality control systems-ER-associated degradation-has been advanced through new structural and functional studies of the core Hrd1 complex, and through the discovery of a new branch of this degradative pathway. New data also reveal how cells resolve clogged translocons, which would otherwise be unable to function. Finally, new work elucidates how mitochondrial tail-anchored proteins that have been mistargeted to the ER are identified and destroyed. Overall, we describe an emerging picture of an increasingly complex quality control network.
Topics: Endoplasmic Reticulum; Membrane Proteins; Protein Folding; Quality Control
PubMed: 33857720
DOI: 10.1016/j.sbi.2021.03.003 -
Bioinformatics (Oxford, England) Nov 2021Cell-free DNA (cfDNA) is gaining substantial attention from both biological and clinical fields as a promising marker for liquid biopsy. Many aspects of disease-related...
MOTIVATION
Cell-free DNA (cfDNA) is gaining substantial attention from both biological and clinical fields as a promising marker for liquid biopsy. Many aspects of disease-related features have been discovered from cfDNA high-throughput sequencing (HTS) data. However, there is still a lack of integrative and systematic tools for cfDNA HTS data analysis and quality control (QC).
RESULTS
Here, we propose cfDNApipe, an easy-to-use and systematic python package for cfDNA whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data analysis. It covers the entire analysis pipeline for the cfDNA data, including raw sequencing data processing, QC and sophisticated statistical analysis such as detecting copy number variations (CNVs), differentially methylated regions and DNA fragment size alterations. cfDNApipe provides one-command-line-execution pipelines and flexible application programming interfaces for customized analysis.
AVAILABILITY AND IMPLEMENTATION
https://xwanglabthu.github.io/cfDNApipe/.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Sequence Analysis, DNA; Cell-Free Nucleic Acids; DNA Copy Number Variations; High-Throughput Nucleotide Sequencing; Quality Control
PubMed: 34042972
DOI: 10.1093/bioinformatics/btab413 -
JBRA Assisted Reproduction May 2020
Topics: Fertilization in Vitro; Humans; Quality Control; Reproductive Medicine
PubMed: 32301598
DOI: 10.5935/1518-0557.20200021 -
Cold Spring Harbor Perspectives in... Mar 2017Maintaining functional protein homeostasis (proteostasis) is a constant challenge in the face of limited protein-folding capacity, environmental threats, and aging.... (Review)
Review
Maintaining functional protein homeostasis (proteostasis) is a constant challenge in the face of limited protein-folding capacity, environmental threats, and aging. Cells have developed several quality-control mechanisms that assist nascent polypeptides to fold properly, clear misfolded molecules, respond to the accumulation of protein aggregates, and deposit potentially toxic conformers in designated sites. Proteostasis collapse can lead to the development of diseases known as proteinopathies. Here we delineate the current knowledge on the different layers of protein quality-control mechanisms at the organelle and cellular levels with an emphasis on the prion protein (PrP). We also describe how protein quality control is integrated at the organismal level and discuss future perspectives on utilizing proteostasis maintenance as a strategy to develop novel therapies for the treatment of proteinopathies.
Topics: Humans; Quality Control; Unfolded Protein Response
PubMed: 27864315
DOI: 10.1101/cshperspect.a023523 -
Journal of Pharmaceutical and... Jan 2021Issues related to pharmaceutical quality are arising at an alarming rate. Pharmaceutical quality concerns both the Active Pharmaceutical Ingredients (APIs) and the... (Review)
Review
Issues related to pharmaceutical quality are arising at an alarming rate. Pharmaceutical quality concerns both the Active Pharmaceutical Ingredients (APIs) and the Finished Drug Product/ Formulation. Recently, there has been a significant increase in the number of reports of harmful impurities in marketed drug formulations. Impurities range from solvents, reactants, adulterants, and catalysts to synthetic byproducts. Quality concerns in commercial preparations may also arise due to shelf life stability. Furthermore, a number of falsified and substandard drug cases have been reported. Most of the techniques which are currently in place can, at best, detect the impurities, but cannot identify them unless they are already known and can be compared to a standard. On the other hand, H NMR spectroscopy detects all the hydrogen containing species, typically provides information to elucidate structures partially or even completely, and through its absolute quantitative capabilities even can detect the presence hydrogen-free species indirectly. The structural properties that produce H NMR signals as characteristic representations of a given molecule are the chemical shifts (δ in ppm) and coupling constants (J in Hz). Along with the line widths (ω in Hz), these parameters are bound to both the molecule and the NMR experimental conditions by quantum mechanical (QM) principles. This means that the H NMR spectra of APIs can be precisely calculated and compared to the experimental data. This review explains how H NMR spectroscopy coupled with Full Spin Analysis can contribute towards the quality control of pharmaceuticals by improving structural dereplication and achieving simultaneous quantification of both APIs and their contaminants.
Topics: Hydrogen; Magnetic Resonance Imaging; Magnetic Resonance Spectroscopy; Pharmaceutical Preparations; Quality Control
PubMed: 33049645
DOI: 10.1016/j.jpba.2020.113601 -
Chemical & Pharmaceutical Bulletin Oct 2016Recent active research and new regulatory guidance on pharmaceutical cocrystals have increased the rate of their development as promising approaches to improve handling,... (Review)
Review
Recent active research and new regulatory guidance on pharmaceutical cocrystals have increased the rate of their development as promising approaches to improve handling, storage stability, and bioavailability of poorly soluble active pharmaceutical ingredients (APIs). However, their complex structure and the limited amount of available information related to their performance may require development strategies that differ from those of single-component crystals to ensure their clinical safety and efficacy. This article highlights current methods of characterizing pharmaceutical cocrystals and approaches to controlling their quality. Different cocrystal regulatory approaches between regions are also discussed. The physical characterization of cocrystals should include elucidating the structure of their objective crystal form as well as their possible variations (e.g., polymorphs, hydrates). Some solids may also contain crystals of individual components. Multiple processes to prepare pharmaceutical cocrystals (e.g., crystallization from solutions, grinding) vary in their applicable ingredients, scalability, and characteristics of resulting solids. The choice of the manufacturing method affects the quality control of particular cocrystals and their formulations. In vitro evaluation of the properties that govern clinical performance is attracting increasing attention in the development of pharmaceutical cocrystals. Understanding and mitigating possible factors perturbing the dissolution and/or dissolved states, including solution-mediated phase transformation (SMPT) and precipitation from supersaturated solutions, are important to ensure the bioavailability of orally administrated lower-solubility APIs. The effect of polymer excipients on the performance of APIs emphasizes the relevance of formulation design for appropriate use.
Topics: Chemistry, Pharmaceutical; Crystallization; Pharmaceutical Preparations; Quality Control
PubMed: 27319284
DOI: 10.1248/cpb.c16-00233 -
Journal of Applied Clinical Medical... Mar 2023The historic and ongoing evolution of the practice, technology, terminology, and implementation of programs related to quality in the medical radiological professions...
The historic and ongoing evolution of the practice, technology, terminology, and implementation of programs related to quality in the medical radiological professions has given rise to the interchangeable use of the terms Quality Management (QM), Quality Assurance (QA), and Quality Control (QC) in the vernacular. This White Paper aims to provide clarification of QM, QA, and QC in medical physics context and guidance on how to use these terms appropriately in American College of Radiology (ACR) Practice Parameters and Technical Standards, generalizable to other guidance initiatives. The clarification of these nuanced terms in the radiology, radiation oncology, and nuclear medicine environments will not only boost the comprehensibility and usability of the Medical Physics Technical Standards and Practice Parameters, but also provide clarity and a foundation for ACR's clinical, physician-led Practice Parameters, which also use these important terms for monitoring equipment performance for safety and quality. Further, this will support the ongoing development of the professional practice of clinical medical physics by providing a common framework that distinguishes the various types of responsibilities borne by medical physicists and others in the medical radiological environment. Examples are provided of how QM, QA, and QC may be applied in the context of ACR Practice Parameters and Technical Standards.
Topics: Humans; Radiation Oncology; Nuclear Medicine; Radiography; Quality Control; Physics
PubMed: 36659841
DOI: 10.1002/acm2.13885