Softwares

Overview of EPI2ME Labs Workflows

The Nanopore Learning course on Human Genome Sequencing and Analysis had a short video introducing the EPI2ME Labs workflows. Anthony Doran, a Technical Applications Scientist in Bioinformatics at Oxford Nanopore Technologies, spoke about the bioinformatics workflows available in EPI2ME Labs. Workflows were defined as multistep pipelines that may include many software and files at different […]
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The EPI2ME Labs wf-human-variation Workflow

Happy Thanksgiving! Tonight I watched a second video on EPI2ME Labs that is part of the Human genome sequencing and analysis course offered by Nanopore Learning. This half-hour video presented by Bala Periaswamy from Oxford Nanopore spoke about EPI2ME Labs and how it can run workflows through the use of Docker and Nextflow. The wf-human-variation […]
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EPI2ME Labs as a Learning Platform

Tonight I started an EPI2ME Metagenomics workflow to analyze our two 16S runs for the metagenomics class. I also watched the Nanopore Learning Human Genome Sequencing and Analysis course video on “Data Analysis: EPI2ME Labs Introduction.” Anthony Doran, a member of the Technical Services Team with Oxford Nanopore Technologies, described EPI2ME Labs as a “point-and-click” […]
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Epigenetics and DNA Methylation Detection with ONT

Continuing with the Human genome sequencing and analysis Nanopore Learning course, tonight I watched the video on “Methylation Detection: Sample to Answer Workflow Overview.” Dilrini De Silva from the Technical Services Team at Oxford Nanopore started by defining epigenetics as the study of gene activity caused by chemical modification of nucleic acids, both DNA and […]
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Data Analysis Solutions from ONT

The next lesson in the Nanopore Learning course for Human genome sequencing and analysis I watched was the introduction to data analysis solutions video. The speaker, Anthony Doran, shared a graphic with the different bioinformatics options provided by Oxford Nanopore. EPI2ME is the real-time cloud-based platform. There are several workflows for quality control, alignment, and […]
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Gbases and Basecallig

Continuing with the Human genome sequencing and analysis Nanopore Learning course, I watched the session entitled “MinKNOW: Live basecalling and output folder structure.” Marta Verdugo, a member of the Technical Services Team with Oxford Nanopore Technologies, introduced the different data types and how MinKNOW processes signals into reads. Each read corresponds to a signal from […]
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Identifying Methylation States with MinKNOW

Dilrini De Silva, a Technical Applications Scientist in Bioinformatics at Oxford Nanopore Technologies, spoke about Methylation Detection on MinKNOW as part of the Human genome sequencing and analysis Nanopore Learning course. They discussed approaches for detecting methylation states with Nanopore sequencing and the MinKNOW software. MinKNOW includes models for methylation detection and mapping of reads. […]
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