DNA

Plant Genome Assembly Insights from ONT Workshop

Tonight I watched the Oxford Nanopore Technologies (ONT) PAG Industry Workshop session titled “A single-platform solution for plant de novo genome assembly.” Jeannie Mounger, a field applications scientist with ONT, was the presenter. They noted that for plant genome assembly there are several considerations. Plant genome size varies greatly: from Mb to Gb. Polyploidy varies […]
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Exploring Microbial Genomics and Lanthanide Mining

Continuing with the LISA workshop, tonight I watched another session. This one was by a postdoc, Andrew Wilson, at Pacific Northwest National Laboratory. They have been working on plasmid and microbe sequencing. The title of the session was “Leveraging Long Reads for Synthetic Biology.” Wilson and team are using Gibson assembly and synthetic biology techniques. […]
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Exploring N50 and Genome Assembly Techniques in KBase

Tonight I continued watching the LISA workshop videos. Lauren Lui from Laurence Berkley National Lab explained the apps available on KBase for long-read only and hybrid assemblies. Using a KBase narrative, Lui shared a Spades short-read-only assembly with 30~ contigs. They described the N50 as a metric for comparing genome assemblies. To calculate N50, contigs […]
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Understanding Hybrid Assemblies in Genomics Research

Tonight I watched the introduction to day 3 of the LISA workshop. Lauren Liu from Lawrence Berkeley Nation Laboratory spoke about how genomics research can be limited by incomplete genomes. They noted that “genomes are hypotheses about what microbes are doing… but with environmental sequencing we often don’t have complete genomes.” Liu explained that assembly […]
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Insights from KBase LISA: Base Calling in Sequencing

Tonight I started watching the recordings from the KBase LISA workshop. I watched the base calling session by Torben Nielsen from Lawrence Berkeley National Laboratory. Nielsen compared PacBio and Nanopore sequencing. PacBio is sequencing by synthesis with limited length. Base calling is performed by image processing. The native error rate for PacBio is about 15%, […]
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Exploring Metagenomic Tools: Kaiju, GOTTCHA2, and More

Tonight I continued watching the recording for the ISME19 workshop “From Reads to Function” corresponding to the last part of Day 1. Ben Allen from KBase described completeness and contamination of bins/MAGs. The next step in the workflow is taxonomic assessment and classification. First, one option is to classify taxonomy of metagenomic reads with Kaiju. […]
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Understanding Metagenomics Workflows in KBase

I continued watching the ISME19 Workshop “From Reads to Function” day 1 sessions. Next, Ben Allen from KBase spoke about “Metagenomics in KBase.” Allen went over metagenomics workflows in KBase. They explained that the workflow is based on the Chivian et al. (2023) Nature Protocols publication. Allen shared a graph with the NCBI Sequencing Read […]
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