Introduction to Metabarcoding and Metagenomics Analysis workshop, May 8 - 11 The ability to identify organisms from traces of genetic material in environmental samples has reshaped the way we see life on earth. Especially for microorganisms, where traditional identification is hard or near impossible, metagenomic techniques have granted us unprecedented insight into the microbiome of animals and the environment more broadly. Instructors Urmi Trivedi, Head of Bioinformatics, Edinburgh Genomics Heleen De Weerd, Bioinformatician, Edinburgh Genomics Nathan Medd, Training and Outreach Manager, Edinburgh Genomics Workshop format This live online workshop consists of presentations and hands-on tutorials. Who should attend Graduates, postgraduates, and PIs, who are using, or planning to use, metagenomic technology in their research and want to learn how to process and analyse the data produced. Requirements A general understanding of molecular biology and genomics. A working knowledge of Linux at the level of the Edinburgh Genomics Linux for Genomics workshop. Content In this course we will cover the following topics: Metabarcoding: Preprocess metabarcoding data using cutadapt "Import" data into QIIME2 Do quality filtering, denoising and picking of features and representative sequences (ASV) using DADA2 Assign taxonomy to features with trained classifiers. Align sequences and build a phylogenetic tree. Calculate alpha and beta diversity Perform differential abundance analysis between groups using ANCOM Shotgun Metagenomics: Data QC and Preprocessing of short reads Taxonomic profiling using MetaPhlAn3 Functional profiling using HUMAnN3 Metagenome assembly using short reads using megahit Contigs binning and generation of metagenome assembled genomes (MAGs) Quality assessment of MAGs using CheckM De-replication of MAGs Taxonomic classification with GTDB-Tk Data QC and Preprocessing of long reads Metagenome assembly using long reads (Oxford Nanopore) using metaFlye Polishing long read assembly with Marginpolish , HELEN and Racon Assess the quality of assemblies using QUAST and IDEEL Related Link Edinburgh Genomics May 08 2023 10.00 - May 11 2023 15.00 Introduction to Metabarcoding and Metagenomics Analysis workshop, May 8 - 11 The workshop will enable you to identify organisms (especially microorganisms) from traces of genetic material in environmental samples. Register here
Introduction to Metabarcoding and Metagenomics Analysis workshop, May 8 - 11 The ability to identify organisms from traces of genetic material in environmental samples has reshaped the way we see life on earth. Especially for microorganisms, where traditional identification is hard or near impossible, metagenomic techniques have granted us unprecedented insight into the microbiome of animals and the environment more broadly. Instructors Urmi Trivedi, Head of Bioinformatics, Edinburgh Genomics Heleen De Weerd, Bioinformatician, Edinburgh Genomics Nathan Medd, Training and Outreach Manager, Edinburgh Genomics Workshop format This live online workshop consists of presentations and hands-on tutorials. Who should attend Graduates, postgraduates, and PIs, who are using, or planning to use, metagenomic technology in their research and want to learn how to process and analyse the data produced. Requirements A general understanding of molecular biology and genomics. A working knowledge of Linux at the level of the Edinburgh Genomics Linux for Genomics workshop. Content In this course we will cover the following topics: Metabarcoding: Preprocess metabarcoding data using cutadapt "Import" data into QIIME2 Do quality filtering, denoising and picking of features and representative sequences (ASV) using DADA2 Assign taxonomy to features with trained classifiers. Align sequences and build a phylogenetic tree. Calculate alpha and beta diversity Perform differential abundance analysis between groups using ANCOM Shotgun Metagenomics: Data QC and Preprocessing of short reads Taxonomic profiling using MetaPhlAn3 Functional profiling using HUMAnN3 Metagenome assembly using short reads using megahit Contigs binning and generation of metagenome assembled genomes (MAGs) Quality assessment of MAGs using CheckM De-replication of MAGs Taxonomic classification with GTDB-Tk Data QC and Preprocessing of long reads Metagenome assembly using long reads (Oxford Nanopore) using metaFlye Polishing long read assembly with Marginpolish , HELEN and Racon Assess the quality of assemblies using QUAST and IDEEL Related Link Edinburgh Genomics May 08 2023 10.00 - May 11 2023 15.00 Introduction to Metabarcoding and Metagenomics Analysis workshop, May 8 - 11 The workshop will enable you to identify organisms (especially microorganisms) from traces of genetic material in environmental samples. Register here
May 08 2023 10.00 - May 11 2023 15.00 Introduction to Metabarcoding and Metagenomics Analysis workshop, May 8 - 11 The workshop will enable you to identify organisms (especially microorganisms) from traces of genetic material in environmental samples.
