Year: 2024

Enhancing Microbiome Data Collection with NMDC Tools

I’m still watching day 2 of the ISME19 workshop “From Reads to Function.” This session included Iyanu Oduwole, Emile Skoog, and Kent Pham. They introduced NMDC and Sample Metadata. The National Microbiome Data Collaborative (NMDC). Iyanu Oduwole is a Genome Science and Technology Ph.D. candidate at Bredesen Center UTORII. Emilie Skoog is a postdoctoral researcher […]
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Understanding DRAM and Genome Analysis at ISME19

I continue watching the ISME19 KBase workshop: “From Reads to Function, Day 2.” Jared Ellenbogen presented next. They spoke about “DRAM and genome-resolved inference.” Ellenbogen spoke about analyzing the fifteen genomes studied during the workshop with DRAM. The outputs of DRAM were described: a heat map with every row corresponding to a different genome or […]
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Insights into dRep and DRAM Tools for MAGs

Tonight I started watching day 2 of the ISME19 workshop “From Reads to Function.” Mikayla Borton from Colorado State University presented on “DRAM and genome-resolved inference.” Borton started with dereplication of bins/MAGs. After that step, MAGs are annotated with DRAM. The tool used to dereplicate metagenome assembled genomes (MAGs) is dRep. Borton explained that the […]
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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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Metagenomics Explained: From DNA Reads to MAGs

Tonight I continued watching the ISME19 Workshop by KBase: “From Reads to Function, Day 1.” Kelly Wrighton presented on “Metagenomics 101: From Reads to Bins.” Wrighton is at Colorado State. Wrighton co-runs the Microbial Ecosystems Lab. They defined microbiome as “the study of microorganisms, their genomes, and their surrounding chemical and other environmental conditions.” I appreciate how this […]
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GROWdb Project: Sequencing Global River Ecosystems

Tonight I started watching the ISME19 Workshop by KBase: “From Reads to Function, Day 1.” Mikayla Borton was the first speaker of this session. The workshop had twenty-five people in person and ~220 virtual participants… from fifty countries. The KBase Education team was there! Borton’s session was on the Genome Resolved Open Watersheds database (GROWdb) […]
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Highlights from ENIGMA Workshop on Isolate Sequencing

Tonight I watched Lauren Lui from Lawrence Berkley National Laboratory present a “Long Read Isolate Sequencing and Assembly Workshop.” This session was recorded April 2, 2024 and was part of the ENIGMA program. Lui provided an overview of the apps they use: Filtlong, Unicycler, Polypolish, and Flye. The team was motivated by evolving long-read technologies […]
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Long-reads Tools in KBase

I ran out of Nanopore videos on their YouTube channel! So I started watching a KBase webinar on long-read tools. Benjamin Allen from KBase introduced the session. This webinar will help me prepare for BIT 295 and isolate sequencing next semester. Allen shared KBase resources including the YouTube channel webinar recordings and the LISA Workshop […]
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Masterclass on Nanopore Sequencing: Expert Planning Tips

Tonight I watched an updated session entitled “How to get started with nanopore sequencing and plan your experiment.” The speaker was Akelia Wauchope-Odumbo, Associate Director of Technical Applications – Americas with Oxford Nanopore Technologies (ONT). Wauchope-Odumbo started this new masterclass series. The theme is “from sample to answer” covering preparation, sequencing, and analysis. The masterclass […]
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