Authors: Shifu Chen, Yanqing Zhou, Yaru Chen...

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

Authors: Steven W Wingett, Simon Andrews

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

Review

Authors: Wei-Long Hong, He Huang, Xue Zeng...

Mitochondria play a crucial role in maintaining the normal physiological state of cells. Hence, ensuring mitochondrial quality control is imperative for the prevention and treatment of numerous diseases. Previous reviews on this topic have however been inconsistencies and lack of systematic organization. Therefore, this review aims to provide a comprehensive and systematic overview of mitochondrial quality control and explore the possibility of targeting the same for the treatment of major diseases. This review systematically summarizes three fundamental characteristics of mitochondrial quality control, including mitochondrial morphology and dynamics, function and metabolism, and protein expression and regulation. It also extensively examines how imbalances in mitochondrial quality are linked to major diseases, such as ischemia-hypoxia, inflammatory disorders, viral infections, metabolic dysregulations, degenerative conditions, and tumors. Additionally, the review explores innovative approaches to target mitochondrial quality control, including using small molecule drugs that regulate critical steps in maintaining mitochondrial quality, nanomolecular materials designed for precise targeting of mitochondria, and novel cellular therapies, such as vesicle therapy and mitochondrial transplantation. This review offers a novel perspective on comprehending the shared mechanisms underlying the occurrence and progression of major diseases and provides theoretical support and practical guidance for the clinical implementation of innovative therapeutic strategies that target mitochondrial quality control for treating major diseases.

Topics: Humans; Mitochondria; Quality Control; Neoplasms

PubMed: 39164792
DOI: 10.1186/s40779-024-00556-1

Review

Authors: Teresa Kowalska, Mieczysław Sajewicz

The aim of this paper is to present a comprehensive overview of the main aims and scopes in screening of botanicals, a task of which thin-layer chromatography (TLC) is, on an everyday basis, confronted with and engaged in. Stunning omnipresence of this modest analytical technique (both in its standard format (TLC) and the high-performance one (HPTLC), either hyphenated or not) for many analysts might at a first glance appear chaotic and random, with an auxiliary rather than leading role in research, and not capable of issuing meaningful final statements. Based on these reflections, our purpose is not to present a general review paper on TLC in screening of botanicals, but a blueprint rather (illustrated with a selection of practical examples), which highlights a sovereign and important role of TLC in accomplishing the following analytical tasks: (i) solving puzzles related to chemotaxonomy of plants, (ii) screening a wide spectrum of biological properties of plants, (iii) providing quality control of herbal medicines and alimentary and cosmetic products of biological origin, and (iv) tracing psychoactive plants under forensic surveillance.

Topics: Chromatography, Thin Layer; Plants, Medicinal; Quality Control

PubMed: 36235143
DOI: 10.3390/molecules27196607

Review

Authors: Ben P Phillips, Elizabeth A Miller

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

Authors: David Meldrum

Topics: Fertilization in Vitro; Humans; Quality Control; Reproductive Medicine

PubMed: 32301598
DOI: 10.5935/1518-0557.20200021

Review

Authors: Meryeme El Maouardi, Mourad Kharbach, Yahya Cherrah...

In addition to the nutritional and therapeutic benefits, Argan oil is praised for its unique bio-ecological and botanic interest. It has been used for centuries to treat cardiovascular issues, diabetes, and skin infections, as well as for its anti-inflammatory and antiproliferative properties. Argan oil is widely commercialized as a result of these characteristics. However, falsifiers deliberately blend Argan oil with cheaper vegetable oils to make economic profits. This reduces the quality and might result in health issues for consumers. Analytical techniques that are rapid, precise, and accurate are employed to monitor its quality, safety, and authenticity. This review provides a comprehensive overview of studies on the quality assessment of Moroccan Argan oil using both untargeted and targeted approaches. To extract relevant information on quality and adulteration, the analytical data are coupled with chemometric techniques.

Topics: Plant Oils; Food; Quality Control

PubMed: 36838806
DOI: 10.3390/molecules28041818

Review

Authors: Tatyana Dubnikov, Tziona Ben-Gedalya, Ehud Cohen...

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

Authors: Philip Ewels, Måns Magnusson, Sverker Lundin...

MOTIVATION

Fast and accurate quality control is essential for studies involving next-generation sequencing data. Whilst numerous tools exist to quantify QC metrics, there is no common approach to flexibly integrate these across tools and large sample sets. Assessing analysis results across an entire project can be time consuming and error prone; batch effects and outlier samples can easily be missed in the early stages of analysis.

RESULTS

We present 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. MultiQC can plot data from many common bioinformatics tools and is built to allow easy extension and customization.

AVAILABILITY AND IMPLEMENTATION

MultiQC is available with an GNU GPLv3 license on GitHub, the Python Package Index and Bioconda. Documentation and example reports are available at http://multiqc.info

CONTACT

[email protected].

Topics: Computational Biology; High-Throughput Nucleotide Sequencing; Quality Control; Software

PubMed: 27312411
DOI: 10.1093/bioinformatics/btw354

Review

Authors: Ken-Ichi Izutsu, Tatsuo Koide, Noriyuki Takata...

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