Samtools

The cultivated aromatic medicinal herb Atractylodes lancea (Thunb.) DC. is widely used in the pharmaceuticals, nutraceuticals, and cosmetics industries (Na-Bangchang et al. 2014; Zhan et al. 2023). Huanggang in Hubei Province is a major production area for A. lancea (Huang et al. 2022; Wang et al. 2023). In April 2023, more than two-thirds of the surveyed plant leaves in this region exhibited virus-like symptoms, such as curling and mosaic patterns. To identify the underlying cause, 80 symptomatic plant leaf samples were collected from four fields (20 leaves per field) in this region and pooled for virome analysis...

Nucleotide substitutions have played an important role in molecular evolution, and understanding their dynamics would contribute to genetic studies. Related research with defined DNA sequences lasted for decades until whole-genome sequencing arose. UV radiation (UVR) can generate base changes and other genetic variations in a short period of time, so it would be more meaningful to explore mutations caused by UVR from a genomic perspective. The monokaryon enoki strain WT583 was selected as the experimental material in this study because it can spontaneously produce large amounts of oidia on PDA plates, and the monokaryons originating from oidia have the same genotype as their mother monokaryon...

BACKGROUND: Structural variant (SV) calling from DNA sequencing data has been challenging due to several factors, including the ambiguity of short-read alignments, multiple complex SVs in the same genomic region, and the lack of "truth" datasets for benchmarking. Additionally, caller choice, parameter settings, and alignment method are known to affect SV calling. However, the impact of FASTQ read order on SV calling has not been explored for long-read data. RESULTS: Here, we used PacBio DNA sequencing data from 15 Caenorhabditis elegans strains and four Arabidopsis thaliana ecotypes to evaluate the sensitivity of different SV callers on FASTQ read order...

DNA-dependent protein kinase catalytic subunit (DNA-PK) is a multifunctional serine‑threonine protein kinase that plays roles in non-homologous end joining of DNA repair in cells. NU7441 is a specific DNA-PKcs inhibitor. We investigated the effects of NU7441 on the transcriptome of BT549 triple negative breast cancer cells. Total RNA extracted from NU7441-treated or control BT549 cells was processed for preparation of sequencing libraries. Assessment of read quality was performed using fastqc tool. Trimming and filtering low-quality reads were performed using fastp...

The genome-wide analysis of runs of homozygosity (ROH) islands can be an effective strategy for identifying shared variants within a population and uncovering important genomic regions related to complex traits. The current study performed ROH analysis to characterize the genome-wide patterns of homozygosity, identify ROH islands and annotated genes within these candidate regions using whole-genome sequencing data from 100 American mink (Neogale vison). After sequence processing, variants were called using GATK and Samtools pipelines...

BACKGROUND: A filamentous fungus Penicillium rubens is widely recognized for producing industrially important antibiotic, penicillin at industrial scale. OBJECTIVE: To better comprehend, the genetic blueprint of the wild-type P. rubens was isolated from India to identify the genetic/biosynthetic pathways for phenoxymethylpenicillin (penicillin V, PenV) and other secondary metabolites. METHOD: Genomic DNA (gDNA) was isolated, and library was prepared as per Illumina platform...

Metagenomic sequencing is a valuable tool for non-specifically detecting various microorganisms in samples, offering unique advantages for detecting emerging pathogens, fastidious or uncultivable pathogens, and mixed infections. It has recently been applied to clinically detect pathogenic microorganisms in animals; however, the high proportion of host genes, expensive sequencing equipment, and the complexity of sequencing and data analysis methods have limited its clinical utility. In this study, a combination of tissue homogenization and nuclease digestion was employed to remove host genes from pig and cat samples; DNA and RNA were then extracted and subjected to nonselective PCR amplification to simultaneously detect DNA and RNA pathogen genomes using R9...

Herein, we report the mutational spectrum of three breast cancer candidate genes ( TP53 , PIK3CA , and PTEN ) using WES for identifying potential biomarkers. The WES data were thoroughly analyzed using SAMtools for variant calling and identification of the mutations. Various bioinformatic tools (SIFT, PolyPhen-2, Mutation Taster, ISPRED-SEQ, SAAFEQ-SEQ, ConSurf, PROCHECK etc.) were used to determine the pathogenicity and nature of the SNVs. Selected interaction site (IS) mutations were visualized in PyMOL after building 3D structures in Swiss-Model...

BACKGROUND: Processing raw genomic data for downstream applications such as imputation, association studies, and modeling requires numerous third-party bioinformatics software tools. It is highly time-consuming and resource-intensive with computational demands and storage limitations that pose significant challenges that increase cost. The use of software tools independent of one another, in a disjointed stepwise fashion, increases the difficulty and sets forth higher error rates because of fragmented job executions in alignment, variant calling, and/or build conversion complications...

BACKGROUND: Wide resection remains the cornerstone of localized soft-tissue sarcomas (STS) treatment. Neoadjuvant radiation therapy (NRT) may decrease the risk of local recurrences; however, its effectiveness for different histological STS subtypes has not been systematically investigated. The proposed prospective study evaluates the NRT response in STS using liquid biopsies and the correlation of multiparametric magnetic resonance imaging (mpMRI) with histopathology and immunohistochemistry...

Genomic analyses are widely applied to epidemiological, population genetic and experimental studies of pathogenic fungi. A wide range of methods are employed to carry out these analyses, typically without including controls that gauge the accuracy of variant prediction. The importance of tracking outbreaks at a global scale has raised the urgency of establishing high-accuracy pipelines that generate consistent results between research groups. To evaluate currently employed methods for whole-genome variant detection and elaborate best practices for fungal pathogens, we compared how 14 independent variant calling pipelines performed across 35 Candida auris isolates from 4 distinct clades and evaluated the performance of variant calling, single-nucleotide polymorphism (SNP) counts and phylogenetic inference results...

Most genome benchmark studies utilize hg38 as a reference genome (based on Caucasian and African samples) and 'NA12878' (a Caucasian sequencing read) for comparison. Here, we aimed to elucidate whether 1) ethnic match or mismatch between the reference genome and sequencing reads produces a distinct result; 2) there is an optimal workflow for single genome data. We assessed the performance of variant calling pipelines using hg38 and a Korean genome (reference genomes) and two whole-genome sequencing (WGS) reads from different ethnic origins: Caucasian (NA12878) and Korean...

Plastome sequence data is most often extracted from plant whole genome sequencing data and need to be assembled and annotated separately from the nuclear genome sequence. In projects comprising multiple genomes, it is labour intense to individually process the plastomes as it requires many steps and software. This study developed Plastaumatic - an automated pipeline for both assembly and annotation of plastomes, with the scope of the researcher being able to load whole genome sequence data with minimal manual input, and therefore a faster runtime...

BACKGROUND: Although epidermal growth factor (EGF) controls many crucial processes in the human body, it can increase the risk of developing cancer when overexpresses. OBJECTIVES: This study focused on detecting cancer-associated genes that are dysregulated by EGF overexpression. MATERIALS AND METHODS: To identify differentially expressed genes (DEGs), two independent meta-analyses with normal and cancer RNA-Seq samples treated by EGF were conducted...

Objective: There can be extreme variability between individual responses to exercise training, and the identification of genetic variants associated with individual variabilities in exercise-related traits could guide individualized exercise programs. We aimed to screen the exercise-related gene sensitivity of patients with acute myocardial infarction after PCI by establishing the gene spectrum of aerobic exercise and cardiopulmonary function sensitivity, test the effect of individualized precision exercise therapy, and provide evidence for the establishment of a precision medicine program for clinical research...

A common method for quantifying microbial abundances in situ is through metagenomic read recruitment to genomes and normalizing read counts as reads per kilobase (of genome) per million (bases of recruited sequences) (RPKM). We created RRAP (RPKM Recruitment Analysis Pipeline), a wrapper that automates this process using Bowtie2 and SAMtools.

Background: Calcified aortic valve disease (CAVD) is one of the most common valvular heart diseases in the elderly population. However, no effective medical treatments have been found to interfere with the progression of CAVD, and specific molecular mechanisms of CAVD remain unclear. Materials and Methods: Transcriptome sequencing data of GSE55492 and GSE148219 were downloaded from the European Nucleotide Archive, and the microarray dataset, GSE12644 was acquired from the Gene Expression Omnibus database...

De novo mutations (DNMs) are an important cause of genetic disorders. The accurate identification of DNMs from sequencing data is therefore fundamental to rare disease research and diagnostics. Unfortunately, identifying reliable DNMs remains a major challenge due to sequence errors, uneven coverage, and mapping artifacts. Here, we developed a deep convolutional neural network (CNN) DNM caller (DeNovoCNN), that encodes the alignment of sequence reads for a trio as 160$ \times$164 resolution images. DeNovoCNN was trained on DNMs of 5616 whole exome sequencing (WES) trios achieving total 96...

MOTIVATION: Human ancient DNA (aDNA) studies have surged in recent years, revolutionizing the study of the human past. Typically, aDNA is preserved poorly, making such data prone to contamination from other human DNA. Therefore, it is important to rule out substantial contamination before proceeding to downstream analysis. As most aDNA samples can only be sequenced to low coverages (<1x average depth), computational methods that can robustly estimate contamination in the low coverage regime are needed...

The precise detection of causal DNA mutations (deoxyribonucleic acid) is very crucial for forward genetic studies. Several sources of errors contribute to false-positive detections by current variant-calling algorithms, which impact associating phenotypes with genotypes. To improve the accuracy of mutation detection, we implemented a binning method for the accurate detection of likely ethyl methanesulfonate (EMS)-induced mutations in a sequenced mutant population. We also implemented a clustering algorithm for detecting likely false negatives with high accuracy...