HTSQualC is a Flexible and One-Step Quality Control Software for High-throughput Sequencing Data Analysis

Bedre, Renesh; Avila, Carlos A.; Mandadi, Kranthi K.

doi:10.1101/2020.07.23.214536

Cited by 3 publications

(3 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Python version 3.6.10 with the Pandas version 1.0.5 data analysis package was used to implement the equating procedure as outlined in the WinSteps Manual . An analysis of variance (ANOVA) was performed using the Bioinfokit python package, with pairwise differences analyzed using Tukey’s honestly significant difference test …”

Section: Methodsmentioning

confidence: 99%

Statistical Comparison between In-Person and Online General Chemistry Exam Outcomes: A COVID-Induced Case Study

Sorenson,

Hanson

2023

J. Chem. Educ.

View full text Add to dashboard Cite

In spring 2020, the chemical education community faced an abrupt transition from in-person to online classes, which also necessitated online assessments. Building upon an existing three-semester study (F17, S19, and F19) using Rasch modeling and classical testing theory to improve in-person multiple choice exams, this study investigates the impact of online exams (F20, F21, and F22) on assessment quality and student performance in an undergraduate General Chemistry II class. The Cronbach’s alpha and fraction of very good/good questions were found to dramatically increase across the first two semesters (F17 and S19) and then largely plateaued for subsequent exams, regardless of in-person or online test administration. Through the use of linking questions (i.e., repeated questions from semester to semester) and equating procedures, the results indicated that (1) there was not an obvious or uniform increase or decrease in the exam quality or student performance when switching from in-person to online exams and (2) there was no evidence for an increased prevalence of cheating in the unproctored online exam relative to the prior in-person exams. While this data set is not sufficient to make any universal claims, this case study’s outcomes suggest that concerns about increased cheating on unproctored online exams are not inherently founded.

show abstract

Section: Methodsmentioning

confidence: 99%

Statistical Comparison between In-Person and Online General Chemistry Exam Outcomes: A COVID-Induced Case Study

Sorenson,

Hanson

2023

J. Chem. Educ.

View full text Add to dashboard Cite

show abstract

“…Genomic DNA was extracted using the Qiagen Genomic-tip 20/G kit (Qiagen, Hilden, Germany) as previously described 23 and sequenced using an Illumina NextSeq 500 system. Raw reads quality was checked using FastQC 36 . Reads were processed with fastp 0.23.2 (-q 20 -F 15 -f 15) 37 .…”

Section: Methodsmentioning

confidence: 99%

An integrative taxonomy approach reveals Saccharomyces chiloensis sp. nov. as a newly discovered species from Coastal Patagonia

Peña,

Villarreal,

Agier

et al. 2024

Preprint

View full text Add to dashboard Cite

Species delineation in microorganisms is challenging due to the limited markers available for accurate species assignment. Here, we applied an integrative taxonomy approach, combining extensive sampling, whole-genome sequence-based classification, phenotypic profiling, and assessment of interspecific reproductive isolation. Our work reveals the presence of a distinct Saccharomyces lineage in Nothofagus forests of coastal Patagonia. This lineage, designated Saccharomyces chiloensis sp. nov., exhibits 7% genetic divergence from its sister species S. uvarum, as revealed by whole-genome sequencing and population analyses. The South America-C (SA-C) coastal Patagonia population forms a unique clade closely related to a previously described divergent S. uvarum population from Oceania (AUS, found in Australia and New Zealand). Our species reclassification is supported by a low Ortho Average Nucleotide Identity (OANI) of 93% in SA-C and AUS relative to S. uvarum, which falls below the suggested species delineation threshold of 95%, indicating an independent evolutionary lineage. Hybrid spore viability assessment provided compelling evidence that SA-C and AUS are reproductively isolated from S. uvarum. In addition, we found unique structural variants between S. chiloensis sp. nov. lineages, including large-scale chromosomal translocations and inversions, together with a distinct phenotypic profile, emphasizing their intraspecies genetic distinctiveness. We suggest that S. chiloensis sp. nov diverged from S. uvarum in allopatry due to glaciation, followed by post-glacial dispersal, resulting in distinct lineages on opposite sides of the Pacific Ocean. The discovery of S. chiloensis sp. nov. illustrates the uniqueness of Patagonia's coastal biodiversity and underscores the importance of adopting an integrative taxonomic approach in species delineation to unveil cryptic microbial species. The holotype of S. chiloensis sp. nov. is CBS 18620T.

show abstract

“…UseGalaxy webserver ( , accessed on 23 August 2021) was used to convert sequence read archives (SRAs) into FASTQ files with forward and reverse reads. At each step, quality of reads was checked using FASTQC [ 52 ]. For removal of adapter and low-quality sequences from each read, Cutadapt was used [ 53 ].…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification of Stress-Associated Proteins (SAPs) Encoding A20/AN1 Zinc Finger in Almond (Prunus dulcis) and Their Differential Expression during Fruit Development

Fatima

Zafar

Gul

et al. 2021

Plants

View full text Add to dashboard Cite

Stress-associated proteins (SAPs) are zinc finger proteins involved in the regulation of various stresses in a variety of plant species. A total of nine PdSAP genes were identified in Prunus dulcis. Phylogenetic and synteny analyses were performed to analyze the homology and evolutionary relationship of PdSAP genes. The functions of PdSAP genes were assessed by further analyses, including cis-regulatory elements, gene duplication, gene ontology, gene structure, subcellular localization, and motif pattern. This study found that PdSAP genes were unevenly distributed on chromosomes 2, 3, 6, and 7. Phylogenetic analysis of PdSAP genes with Arabidopsis thaliana and Oryza sativa suggested that six subgroups have a similar pattern of AN1 and A20 domains in each subgroup. PdSAP genes lacked duplicated blocks. The majority of PdSAP genes were localized in the nucleus region. Three hormonal and five stress cis-regulatory elements were found in the upstream promoter region of the PdSAP gene family. RNA-seq analysis revealed differential gene expression of PdSAP genes at days 12, 17, 22, 27, 32, and 37 of fruitlet development after flowering. This study identifies the SAP genes in P. dulcis and also provides insights into the expression of PdSAP genes in abnormal fruitlets with diapause atrophic growth at various developmental stages.

show abstract

HTSQualC is a Flexible and One-Step Quality Control Software for High-throughput Sequencing Data Analysis

Cited by 3 publications

References 21 publications

Statistical Comparison between In-Person and Online General Chemistry Exam Outcomes: A COVID-Induced Case Study

Statistical Comparison between In-Person and Online General Chemistry Exam Outcomes: A COVID-Induced Case Study

An integrative taxonomy approach reveals Saccharomyces chiloensis sp. nov. as a newly discovered species from Coastal Patagonia

Genome-Wide Identification of Stress-Associated Proteins (SAPs) Encoding A20/AN1 Zinc Finger in Almond (Prunus dulcis) and Their Differential Expression during Fruit Development

Contact Info

Product

Resources

About