Softwares

The MinKNOW Graphical User Interface (GUI)

Tonight I watched the MinKNOW GUI video from the Nanopore Learning course on Human Genome Sequencing and Analysis. Before watching these videos, I reviewed the Kit 14 videos. The MinKNOW graphical user interface (GUI) session was presented by Marta Verdugo from the Technical Services Team at Oxford Nanopore Technologies (ONT). The MinKNOW software is used […]
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Oxford Nanopore Technologies Kit 14 Options

The Nanopore Learning course on “Human genome sequencing and analysis” has a video on Kit V14. Vania Costa, a Technical Services Specialist with Oxford Nanopore Technologies, described the accuracy of kit 14, which relies on R10.4.1 flow cells and pores. Costa explained that kit v14 has simplex Q20+ and duplex Q30+. Currently, there are ligation-based […]
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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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