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Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data

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Abstract

Identifying and annotating mobile genetic elements (MGE) in metagenomic data can be tricky. To facilitate the process, we can use existing and custom annotated mobile genetic element database.

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

  • How can we use an existing database annotated database to identify and annotate genetic elements in metagenomics data?

Learning Objectives

  • Perform metagenomics read mapping against mobile genetic element database.
  • Evaluate the distribution of mapping scores to identify high-quality alignments.
  • Evaluate plasmid coverage to determine effective filtering thresholds.
  • Filter alignments based on plasmid coverage and mapping quality.
  • Justify the filtering thresholds chosen for identifying plasmid sequences.
  • Generate a curated table of plasmid sequences and convert it into a FASTA file for further analysis.
  • Use tools to process sequences, ensuring data is sorted, deduplicated, and formatted correctly.
  • Annotate features on the identified plasmids using mobile genetic element database annotations.
  • Construct a final annotated dataset integrating genetic element information for downstream applications.

Licence: Creative Commons Attribution 4.0 International

Keywords: Microbiome

Target audience: Students

Resource type: e-learning

Version: 1

Status: Active

Prerequisites:

Introduction to Galaxy Analyses

Learning objectives:

  • Perform metagenomics read mapping against mobile genetic element database.
  • Evaluate the distribution of mapping scores to identify high-quality alignments.
  • Evaluate plasmid coverage to determine effective filtering thresholds.
  • Filter alignments based on plasmid coverage and mapping quality.
  • Justify the filtering thresholds chosen for identifying plasmid sequences.
  • Generate a curated table of plasmid sequences and convert it into a FASTA file for further analysis.
  • Use tools to process sequences, ensuring data is sorted, deduplicated, and formatted correctly.
  • Annotate features on the identified plasmids using mobile genetic element database annotations.
  • Construct a final annotated dataset integrating genetic element information for downstream applications.

Date modified: 2025-01-07

Date published: 2025-01-07

Authors: Bérénice Batut, Didier Debroas, Nadia Goué

Scientific topics: Metagenomics, Microbial ecology, Genomics, Microbiology, Sequence analysis, Mobile genetic elements

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