sequencing

Quality Control of Input DNA RNA

Continuing with the Human genome sequencing and analysis course, today I watched the video lesson on “Library preparation: Quality control of input DNA or RNA.” Hazel Johnson, a Technical Services Team member at Oxford Nanopore Technologies, explained that incorrectly quantifying DNA can result in reduced sequencing input. They do not recommend the use of NanoDrop […]
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Rabbit Blood and Extraction Methods for ONT

The Nanopore Learning course on Human Genome Sequencing and Analysis has a video on Library preparation: Extraction methods and sample handling. Hazel Johnson from the Technical Services Team at Oxford Nanopore Technologies (ONT) spoke about sample extraction methods and considerations. They noted that to go from raw sample to answer, the workflow is not a […]
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An Overview of ONT Devices

Hazel Johnson, member of the Technical Services Team at Oxford Nanopore Technologies, presented the second video in the Nanopore Learning Human Genome Sequencing and Analysis course. They shared the range of products for sample preparation, instruments, and software offered by ONT. Johnson shared a graphic with the nanopore sequencing platforms. The Flongle is low cost […]
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Coverage, Binning, and Dereplication of Metagenomic Data

The last session of the Oxford Nanopore Technologies Nanopore Learning Metagenomics course is about additional metagenomic concepts. Tim Walker spoke about metagenomic assembly: “the computational process which seeks to reconstruct the microbial genomes within a metagenomic mixture.”The assembled reads could be genomes or plasmids. Metagenomic assembled genomes (MAGs) can be used for several analyses. Coverage […]
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MetaQUAST, BUSCO, CheckM, and more Bandage!

Tim Walker explained quality control of metagenomic assemblies as part of the Nanopore Learning Metagenomics course. They spoke about the metrics to determine confidence in assembly model and the information it gives. Walker stated: “… what is truth, and what is artifact” to emphasize the use of metrics for metagenomic assembly quality control. Walker explained […]
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Checking MAGs

The next lesson in the Nanopore Learning Metagenomics course that I watched tonight was “Introduction to metagenomic assembly.” Tim Walker from the Technical Services Group at ONT introduced metagenomic assembly as reconstruction of reads into corresponding genomes. Metagenomic assembly is a computational process, said Walker, and the contigs may resemble the genomes or plasmids. Metagenome […]
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The Cloud-based EPI2ME Metagenomics Workflows

Tim Walker from the Technical Services Group conducted a demonstration of EPI2ME as part of the Nanopore Learning course. Walker noted that EPI2ME currently hosts free metagenomic classification pipelines including WIMP, the antimicrobial resistance workflow, and the Fastq 16S workflow. The 16S workflow works with the 16S barcoding kit. This is the kit and workflow […]
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Metagenomic Classification and ONT Reads

Tim Walker from the Technical Services Team with Oxford Nanopore Technologies presented the Nanopore Learning Course – Metagenomics lesson I watched tonight. They spoke about metagenomic classification techniques to identify organisms from sequence data and annotate genes. For targeted metagenomics, ITS, 16S, or antibiotic resistance genes can be amplified and sequenced. Whole genome sequencing can […]
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MinKNOW Features and Run Assessment

Marta Verdugo from Oxford Nanopore Technologies is the presenter for the Nanopore Learning sessions I watched tonight. The series of videos focused on MinKNOW and setting up an experiment. Verdugo provided an overview of the MinKNOW graphical user environment. In the second video of the series, they set up a control experiment. One experiment setup […]
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