CheckQC: Quick quality control of Illumina sequencing runs

Åslin, Matilda; Brandt, Monika; Dahlberg, Johan

doi:10.21105/joss.00556

Cited by 2 publications

(1 citation statement)

References 5 publications

(2 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Bioinformatic data pre-processing, quality control, and mapping Raw sequencing data were then converted by Macrogen into FASTQ files using the conversion software bcl2fastq 84 . Adaptors were clipped using the software cutadapt (v2.4, 85 ), and using Trimmomatic (v.0.39, 86 ) adaptorclipped reads were then quality-filtered through a sliding window approach https://doi.org/10.1038/s42003-024-05926-y Article of 10-base wide window for an average quality of at least Q20 within the window.…”

Section: Determination Of Social Rank and The Two Social Classesmentioning

confidence: 99%

Epigenetic signatures of social status in wild female spotted hyenas (Crocuta crocuta)

Vullioud,

Benhaiem,

Meneghini

et al. 2024

Commun Biol

View full text Add to dashboard Cite

In mammalian societies, dominance hierarchies translate into inequalities in health, reproductive performance and survival. DNA methylation is thought to mediate the effects of social status on gene expression and phenotypic outcomes, yet a study of social status-specific DNA methylation profiles in different age classes in a wild social mammal is missing. We tested for social status signatures in DNA methylation profiles in wild female spotted hyenas (Crocuta crocuta), cubs and adults, using non-invasively collected gut epithelium samples. In spotted hyena clans, female social status influences access to resources, foraging behavior, health, reproductive performance and survival. We identified 149 differentially methylated regions between 42 high- and low-ranking female spotted hyenas (cubs and adults). Differentially methylated genes were associated with energy conversion, immune function, glutamate receptor signalling and ion transport. Our results provide evidence that socio-environmental inequalities are reflected at the molecular level in cubs and adults in a wild social mammal.

show abstract

Section: Determination Of Social Rank and The Two Social Classesmentioning

confidence: 99%

Epigenetic signatures of social status in wild female spotted hyenas (Crocuta crocuta)

Vullioud,

Benhaiem,

Meneghini

et al. 2024

Commun Biol

View full text Add to dashboard Cite

show abstract

Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samples

de Souza,

de Oliveira,

Sales

et al. 2023

Journal of Genetic Engineering and Biotechnology

View full text Add to dashboard Cite

New-generation sequencing (NGS) techniques have brought the opportunity for genomic monitoring of several microorganisms potentially relevant to public health. The establishment of different methods with different mechanisms provides a wide choice, taking into account several aspects. With that in mind, the present aim of the study was to compare basic genomic sequencing metrics that could potentially impact genotyping by nanopores from Oxford Nanopore Technologies and by synthesis from Illumina in clinical samples positive for Chikungunya (CHIKV). Among the metrics studied, running time, read production, and Q score were better represented in Illumina sequencing, while the MinIOn platform showed better response time and greater diversity of generated files. That said, it was possible to establish differences between the studied metrics in addition to verifying that the distinctions in the methods did not impact the identification of the CHIKV virus genotype.

show abstract

CheckQC: Quick quality control of Illumina sequencing runs

Cited by 2 publications

References 5 publications

Epigenetic signatures of social status in wild female spotted hyenas (Crocuta crocuta)

Epigenetic signatures of social status in wild female spotted hyenas (Crocuta crocuta)

Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samples

Contact Info

Product

Resources

About