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Keywords: Exploratory-analysis  or metagenomics  or Chip-seq  or Phylogenetics 


Chip-seq: Motif Analysis Tutorial

Introduction Goal The aim is to : Get familiar with motif analysis of ChIP-seq data. Learn de novo motif discovery methods. In practice : Motif discovery with peak-motifs Differential analysis Random controls

Keywords: Chip-seq, Motif analysis, NGS, Pattern recognition

Chip-seq: Motif Analysis Tutorial https://tess.elixir-europe.org/materials/chip-seq-motif-analysis-tutorial Introduction Goal The aim is to : Get familiar with motif analysis of ChIP-seq data. Learn de novo motif discovery methods. In practice : Motif discovery with peak-motifs Differential analysis Random controls Chip-seq, Motif analysis, NGS, Pattern recognition
Chip-seq: Functional Annotation tutorial

Global Objective Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms.

Keywords: Chip-seq, Functional Annotation, NGS

Chip-seq: Functional Annotation tutorial https://tess.elixir-europe.org/materials/chip-seq-functional-annotation-tutorial Global Objective Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms. Chip-seq, Functional Annotation, NGS
Introducing Bivi.co

Introduction to the Bivi community presented as the introductory talk at the 1st Bivi Annual Meeting. Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations

Resource type: Video

Introducing Bivi.co https://tess.elixir-europe.org/materials/introducing-bivi-co Introduction to the Bivi community presented as the introductory talk at the 1st Bivi Annual Meeting. Created at: 1st BiVi Annual Meeting. Prof. Jessie Kennedy Phylogenetics Pathway or network Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations 2016-12-08
Jalview

Dr James Proctor of the University of Dundee discusses the Jalview tool in the Vis Tools & Bio Challenges session of the 1st BiVi Annual Meeting Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics

Keywords: Genome, Molecular, Phylogenetics

Resource type: Poster, Video

Jalview https://tess.elixir-europe.org/materials/jalview Dr James Proctor of the University of Dundee discusses the Jalview tool in the Vis Tools & Bio Challenges session of the 1st BiVi Annual Meeting Created at: 1st BiVi Annual Meeting. Dr. Jim Procter Jalview Coordinator Phylogenetics Genome, Molecular, Phylogenetics 2016-12-08
BiVi Genomes theme

Prof David Burt introduces the Genomes theme in bio-visualisation. Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics

Keywords: Genome, Phylogenetics

Resource type: Video

BiVi Genomes theme https://tess.elixir-europe.org/materials/bivi-genomes-theme Prof David Burt introduces the Genomes theme in bio-visualisation. Created at: 1st BiVi Annual Meeting. Prof. David Willaim Burt PhD BSc FSB Phylogenetics Genome, Phylogenetics 2016-12-08
Metagenomics

Susannah Tringe talks about metagenomics analysis tools and the challenges of gaining a systems-level understanding of a microbial community. She notes that there are some good analysis tools available for analysis at the 16S sequence and unassembled metagenome level, but more effort into...

Scientific topics: Phylogenetics

Keywords: Genome, Phylogenetics, Populations

Resource type: Video

Metagenomics https://tess.elixir-europe.org/materials/metagenomics-6625dde2-a7da-4cc2-a51d-14c1c31b51b2 Susannah Tringe talks about metagenomics analysis tools and the challenges of gaining a systems-level understanding of a microbial community. She notes that there are some good analysis tools available for analysis at the 16S sequence and unassembled metagenome level, but more effort into analysis and visualisation solutions are required at the microbial community and ecosystem level.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Phylogenetics Genome, Phylogenetics, Populations 2017-01-31
Geographic & Evolutionary Visualization

Daniel Janies showcases SupraMap, a web-based app that integrates genetic sequences of pathogens with geographic data points to map the spread of diseases and track mutations.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013.

Scientific topics: Phylogenetics

Keywords: Phylogenetics, Populations

Resource type: Video

Geographic & Evolutionary Visualization https://tess.elixir-europe.org/materials/geographic-amp-evolutionary-visualization Daniel Janies showcases SupraMap, a web-based app that integrates genetic sequences of pathogens with geographic data points to map the spread of diseases and track mutations.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Phylogenetics Phylogenetics, Populations 2017-01-31
BBSRC: Data and Data Visualisation

Michael Ball from BBSRC's closing remarks on Data and Data Visualisation from 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Information visualisation

Resource type: Video

BBSRC: Data and Data Visualisation https://tess.elixir-europe.org/materials/bbsrc-data-and-data-visualisation Michael Ball from BBSRC's closing remarks on Data and Data Visualisation from 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting. Michael Ball Phylogenetics Pathway or network Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Information visualisation 2017-02-01
BiVi theme: Phylogenetics

Prof Rod Page discusses bio-visualisation and the Phylogenetics theme at 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics

Keywords: Phylogenetics

Resource type: Video

BiVi theme: Phylogenetics https://tess.elixir-europe.org/materials/bivi-theme-phylogenetics Prof Rod Page discusses bio-visualisation and the Phylogenetics theme at 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting. Prof. Rod Page Phylogenetics Phylogenetics 2017-02-02
Aequatus-vis

Anil Thanki describes the Aequatus-vis JavaScript plugin to visualise homologous genes through alignment and phylogeny information at 2nd BiVi in 2015. aequatus-vis preserves teh interactive functionality of Aequatus, an open-source web based tool to visualise homologous genes with phylogenetic...

Scientific topics: Phylogenetics

Keywords: Genome, Phylogenetics

Resource type: Slideshow

Aequatus-vis https://tess.elixir-europe.org/materials/aequatus-vis Anil Thanki describes the Aequatus-vis JavaScript plugin to visualise homologous genes through alignment and phylogeny information at 2nd BiVi in 2015. aequatus-vis preserves teh interactive functionality of Aequatus, an open-source web based tool to visualise homologous genes with phylogenetic tree . Created at: 2nd BiVi Annual Meeting. Anil S. Thanki Phylogenetics Genome, Phylogenetics 2017-02-03
Joint visualisation and analysis of large sequence data with Alvis and Sequence Bundles

Roland Schwarz's keynote about the joint visualisation and analysis of large sequence data with Alvis and Sequence Bundles at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting.

Scientific topics: Phylogenetics

Keywords: Genome, Phylogenetics

Resource type: Slideshow

Joint visualisation and analysis of large sequence data with Alvis and Sequence Bundles https://tess.elixir-europe.org/materials/joint-visualisation-and-analysis-of-large-sequence-data-with-alvis-and-sequence-bundles Roland Schwarz's keynote about the joint visualisation and analysis of large sequence data with Alvis and Sequence Bundles at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting. Dr. Roland Schwarz Phylogenetics Genome, Phylogenetics 2017-02-03
BioJS

Dr Manuel Corpas discusses the BioJS Javascript component library at the 1st BiVi Annual Meeting in 2014. Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Genome, Molecular, Pathway, Phylogenetics

Resource type: Video

BioJS https://tess.elixir-europe.org/materials/biojs-6f4125d4-aca1-407d-b0c7-02345f3b3900 Dr Manuel Corpas discusses the BioJS Javascript component library at the 1st BiVi Annual Meeting in 2014. Created at: 1st BiVi Annual Meeting. Dr. Manuel Corpas Phylogenetics Pathway or network Anatomy Physiology and Atlases, Genome, Molecular, Pathway, Phylogenetics 2016-12-08
Art and Science: A partnership catalyzing discovery in biomedicine

A 3rd BiVi 2017 Keynote Presentation by Bang Wong, Broad Institute of MIT & Harvard and Department of Art as Applied to Medicine, Johns Hopkins University School of MedicineChaired by: Geoff BartonThe data generated by the biomedical research community hold tremendous potential to inform our...

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Communication, Information visualisation

Resource type: Video

Art and Science: A partnership catalyzing discovery in biomedicine https://tess.elixir-europe.org/materials/art-and-science-a-partnership-catalyzing-discovery-in-biomedicine A 3rd BiVi 2017 Keynote Presentation by Bang Wong, Broad Institute of MIT & Harvard and Department of Art as Applied to Medicine, Johns Hopkins University School of MedicineChaired by: Geoff BartonThe data generated by the biomedical research community hold tremendous potential to inform our understanding and treatment of disease. The challenge is to ensure that technical and non-technical researchers can access, use and learn from this wealth of data and analytical resources. Bang will present examples of solutions developed at the Broad Institute that draw on art and design to enable scientific discovery.Bang Wong is the creative director of the Broad Institute of MIT & Harvard and an adjunct assistant professor in the Department of Art as Applied to Medicine at the Johns Hopkins University School of Medicine. His work focuses on the design and development of computation-visualization tools to meet the analytical challenges of research data. He leads the data visualization initiative at the Broad and is the founding author of Points of View published by Nature Methods, a series of articles that focus on the fundamental aspects of data presentation in science. Created at: 3rd BiVi Annual Meeting (2017). Bang Wong Phylogenetics Pathway or network Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Communication, Information visualisation 2017-05-12
ViCTree-Virus Taxonomy Classification Framework

Poster presentation at 3rd BiVi in April 2017. Created at: 3rd BiVi Annual Meeting (2017).

Scientific topics: Phylogenetics

Keywords: Phylogenetics

Resource type: Poster

ViCTree-Virus Taxonomy Classification Framework https://tess.elixir-europe.org/materials/victree-virus-taxonomy-classification-framework Poster presentation at 3rd BiVi in April 2017. Created at: 3rd BiVi Annual Meeting (2017). Ms. Sejal Modha Phylogenetics Phylogenetics 2017-05-30
A Simple Phylogenetic Tree Construction (part 2)

Understand the method used in identifying an unknown sequence. Understand the limitations of this method Get to grips with various software (CLUSTALw, SeaView, Phylo_win and Njplot)

Keywords: Phylogenetics

A Simple Phylogenetic Tree Construction (part 2) https://tess.elixir-europe.org/materials/a-simple-phylogenetic-tree-construction-part-2 Understand the method used in identifying an unknown sequence. Understand the limitations of this method Get to grips with various software (CLUSTALw, SeaView, Phylo_win and Njplot) Phylogenetics
Chip-seq: Pattern Analysis tutorial

Goal The aim is to : Get familiar with motif analysis of ChIP-seq data. Learn de novo motif discovery methods. In practice : Motif discovery with peak-motifs Differential analysis Random controls

Keywords: Chip-seq, NGS, Pattern recognition

Chip-seq: Pattern Analysis tutorial https://tess.elixir-europe.org/materials/chip-seq-pattern-analysis-tutorial Goal The aim is to : Get familiar with motif analysis of ChIP-seq data. Learn de novo motif discovery methods. In practice : Motif discovery with peak-motifs Differential analysis Random controls Chip-seq, NGS, Pattern recognition
A Simple Phylogenetic Tree Construction (part 1)

Understand the method behind constructing a phylogenetic tree from the search for sequences to the analysis of the tree. Get to grips with various bio-informatic software (BLAST, CLUSTALw, SeaView and Phylo_win).

Keywords: Phylogenetics

A Simple Phylogenetic Tree Construction (part 1) https://tess.elixir-europe.org/materials/a-simple-phylogenetic-tree-construction-part-1 Understand the method behind constructing a phylogenetic tree from the search for sequences to the analysis of the tree. Get to grips with various bio-informatic software (BLAST, CLUSTALw, SeaView and Phylo_win). Phylogenetics
Chip-seq: Peak calling tutorial

The aim is to : Understand how to process reads to obtain peaks (peak-calling). Become familiar with differential analysis of peaks In practice : Obtain dataset from GEO Analyze mapped reads Obtain set(s) of peaks, handle replicates Differential analysis of peak

Keywords: Chip-seq, NGS, Peak calling

Chip-seq: Peak calling tutorial https://tess.elixir-europe.org/materials/chip-seq-peak-calling-tutorial The aim is to : Understand how to process reads to obtain peaks (peak-calling). Become familiar with differential analysis of peaks In practice : Obtain dataset from GEO Analyze mapped reads Obtain set(s) of peaks, handle replicates Differential analysis of peak Chip-seq, NGS, Peak calling
Chip Seq: Annotation and visualization Lesson

How to add biological meaning to peaks

Keywords: Annotation, Chip-seq, Data Visualization, NGS

Chip Seq: Annotation and visualization Lesson https://tess.elixir-europe.org/materials/chip-seq-annotation-and-visualization-lesson How to add biological meaning to peaks Annotation, Chip-seq, Data Visualization, NGS
Chip-seq Analysis

Quality, normalisation and peak calling

Keywords: Chip-seq, Genomics

Chip-seq Analysis https://tess.elixir-europe.org/materials/chip-seq-analysis Quality, normalisation and peak calling Chip-seq, Genomics
Chip Seq: Annotation and visualization Tutorial

Global Objective Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms.

Keywords: Annotation, Chip-seq, Data Visualization, NGS

Chip Seq: Annotation and visualization Tutorial https://tess.elixir-europe.org/materials/chip-seq-annotation-and-visualization-tutorial Global Objective Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms. Annotation, Chip-seq, Data Visualization, NGS
Phylogenetics & Phylogeography (Advanced Analytical Methods)

Phylogenetics and Phylogeography(Advanced Analytical Methods) Lecture by Dr Sam Lycett, filmed at The Roslin Institute, March 2015.

Keywords: Phylogenetics, Roslin Institute

Phylogenetics & Phylogeography (Advanced Analytical Methods) https://tess.elixir-europe.org/materials/phylogenetics-phylogeography-advanced-analytical-methods Phylogenetics and Phylogeography(Advanced Analytical Methods) Lecture by Dr Sam Lycett, filmed at The Roslin Institute, March 2015. Phylogenetics, Roslin Institute
Phylogenetics & Phylogeography Practical (Advanced Analytical Methods)

Practical session with Dr Sam Lycett, filmed at The Roslin Institute, March 2015.

Keywords: Phylogenetics, Phylogeography, Roslin Institute

Phylogenetics & Phylogeography Practical (Advanced Analytical Methods) https://tess.elixir-europe.org/materials/phylogenetics-phylogeography-practical-advanced-analytical-methods Practical session with Dr Sam Lycett, filmed at The Roslin Institute, March 2015. Phylogenetics, Phylogeography, Roslin Institute
Who is doing what on the cheese surface? Overview of the cheese microbial ecosystem functioning by metatranscriptomic analyses

Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a...

Keywords: metagenomics

Who is doing what on the cheese surface? Overview of the cheese microbial ecosystem functioning by metatranscriptomic analyses https://tess.elixir-europe.org/materials/who-is-doing-what-on-the-cheese-surface-overview-of-the-cheese-microbial-ecosystem-functioning-by-metatranscriptomic-analyses-55c4b5d0-ba6e-4ae0-879f-7bc27c10b3eb Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on surface-ripened cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We used an iterative sensory procedure to select a simplified microbial consortium, composed of only nine species (three yeasts and six bacteria), producing the odor of Livarot-type cheese when inoculated in a sterile cheese curd. All the genomes were sequenced in order to determine the functional capacities of the different species and facilitate RNA-Seq data analyses. We followed the ripening process of experimental cheeses made using this consortium during four weeks, by metatranscriptomic and biochemical analyses. By combining all of the data, we were able to obtain an overview of the cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. We next applied the same approach to investigate the activity of the microorganisms in real cheeses, namely Reblochon-style cheeses. This provided useful insights into the physiological changes that occur during cheese ripening, such as changes in energy substrates, anabolic reactions, or stresses. metagenomics 2016-12-15 2017-01-11
Welcome message

Presentation of the workshop (Chairman: Claudine Médigue)

Keywords: metagenomics

Welcome message https://tess.elixir-europe.org/materials/welcome-message-69dc597e-f839-448f-9c9d-3622ddffd592 Presentation of the workshop (Chairman: Claudine Médigue) metagenomics 2016-12-15 2017-01-11
Soil metagenomics, potential and pitfalls

The soil microorganisms are responsible for a range of critical functions including those that directly affect our quality of life (e.g., antibiotic production and resistance – human and animal health, nitrogen fixation -agriculture, pollutant degradation – environmental bioremediation)....

Keywords: metagenomics

Soil metagenomics, potential and pitfalls https://tess.elixir-europe.org/materials/soil-metagenomics-potential-and-pitfalls-04d3bb46-36ba-47c0-9993-9c7d0aacad32 The soil microorganisms are responsible for a range of critical functions including those that directly affect our quality of life (e.g., antibiotic production and resistance – human and animal health, nitrogen fixation -agriculture, pollutant degradation – environmental bioremediation). Nevertheless, genome structure information has been restricted by a large extent to a small fraction of cultivated species. This limitation can be circumvented now by modern alternative approaches including metagenomics or single cell genomics. Metagenomics includes the data treatment of DNA sequences from many members of the microbial community, in order to either extract a specific microorganism’s genome sequence or to evaluate the community function based on the relative quantities of different gene families. In my talk I will show how these metagenomic datasets can be used to estimate and compare the functional potential of microbial communities from various environments with a special focus on antibiotic resistance genes. However, metagenomic datasets can also in some cases be partially assembled into longer sequences representing microbial genetic structures for trying to correlate different functions to their co-location on the same genetic structure. I will show how the microbial community composition of a natural grassland soil characterized by extremely high microbial diversity could be managed for sequentially attempt to reconstruct some bacterial genomes. Metagenomics can also be used to exploit the genetic potential of environmental microorganisms. I will present an integrative approach coupling rrs phylochip and high throughput shotgun sequencing to investigate the shift in bacterial community structure and functions after incubation with chitin. In a second step, these functions of potential industrial interest can be discovered by using hybridization of soil metagenomic DNA clones spotted on high density membranes by a mix of oligonucleotide probes designed to target genes encoding for these enzymes. After affiliation of the positive hybridizing spots to the corresponding clones in the metagenomic library the inserts are sequenced, DNA assembled and annotated leading to identify new coding DNA sequences related to genes of interest with a good coverage but a low similarity against closest hits in the databases confirming novelty of the detected and cloned genes. metagenomics 2016-12-16 2017-01-11
Sequencing 6000 chloroplast genomes : the PhyloAlps project

Biodiversity is now commonly described by DNA based approches. Several actors are currently using DNA to describe biodiversity, and most of the time they use different genetic markers that is hampering an easy sharing of the accumulated knowledges. Taxonomists rely a lot on the DNA Barcoding...

Keywords: metagenomics

Sequencing 6000 chloroplast genomes : the PhyloAlps project https://tess.elixir-europe.org/materials/sequencing-6000-chloroplast-genomes-the-phyloalps-project-a2b30d75-061a-4663-a5b8-593842df23bf Biodiversity is now commonly described by DNA based approches. Several actors are currently using DNA to describe biodiversity, and most of the time they use different genetic markers that is hampering an easy sharing of the accumulated knowledges. Taxonomists rely a lot on the DNA Barcoding initiative, phylogeneticists often prefer markers with better phylogenic properties, and ecologists, with the coming of the DNA metabarcoding, look for a third class of markers easiest to amplify from environmental DNA. Nevertheless they have all the same need of the knowledge accumulated by the others. But having different markers means that the sequecences have been got from different individuals in differente lab, following various protocoles. On that base, building a clean reference database, merging for each species all the available markers becomes a challenge. With the phyloAlps project we implement genome skimming at a large scale and propose it as a new way to set up such universal reference database usable by taxonomists, phylogeneticists, and ecologists. The Phyloalps project is producing for each species of the Alpine flora at least a genome skim composed of six millions of 100bp sequence reads. From such data it is simple to extract all chloroplastic, mitochondrial and nuclear rDNA markers commonely used. Moreover, most of the time we can get access to the complete chloroplast genome sequence and to a shallow sequencing of many nuclear genes. This methodes have already been successfully applied to algeae, insects and others animals. With the new single cell sequencing methods it will be applicable to most of the unicellular organisms. The good question is now : Can we consider the genome skimming as the next-generation DNA barcode ? metagenomics 2016-12-16 2017-01-11
From Samples to Data : Assuring Downstream Analysis with Upstream Planning

Metagenomic studies have gained increasing popularity in the years since the introduction of next generation sequencing. NGS allows for the production of millions of reads for each sample without the intermediate step of cloning. However, just as in the past, the quality of the data generate by...

Keywords: metagenomics

From Samples to Data : Assuring Downstream Analysis with Upstream Planning https://tess.elixir-europe.org/materials/from-samples-to-data-assuring-downstream-analysis-with-upstream-planning-6fac0f49-b453-4c15-a409-9753fb27ee9b Metagenomic studies have gained increasing popularity in the years since the introduction of next generation sequencing. NGS allows for the production of millions of reads for each sample without the intermediate step of cloning. However, just as in the past, the quality of the data generate by this powerful technology depends on sample preparation, library construction and the selection of appropriate sequencing technology and sequencing depth. Here we explore the different variables involved in the process of preparing samples for sequencing analysis including sample collection, DNA extraction and library construction. We also examine the various sequencing technologies deployed for routine metagenomic analysis and considerations for their use in different model systems including humans, mouse and the environment. Future developments such as long-reads will also be discussed to provide a complete picture of important aspects prior to data analyses which play a critical role in the success of metagenomic studies. metagenomics 2017-01-11
Revealing and analyzing microbial networks: from topology to functional behaviors

Understanding the interactions between microbial communities and their environment well enough to be able to predict diversity on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. However, modeling microbial communities is a complicated...

Keywords: metagenomics

Revealing and analyzing microbial networks: from topology to functional behaviors https://tess.elixir-europe.org/materials/revealing-and-analyzing-microbial-networks-from-topology-to-functional-behaviors-14d83c7f-c5f9-4738-8cd5-42e48a1088f7 Understanding the interactions between microbial communities and their environment well enough to be able to predict diversity on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. However, modeling microbial communities is a complicated task, because (i) communities are complex, (ii) most are described qualitatively, and (iii) quantitative understanding of the way communities interacts with their surroundings remains incomplete. Within this seminar, we will illustrate two complementary approaches that aim to overcome these points in different manners. metagenomics 2016-12-16 2017-01-11
Reconstructing genomes from metagenomes: The holy grail of microbiology

Shotgun metagenomics provides insights into a larger context of naturally occurring microbial genomes when short reads are assembled into contiguous DNA segments (contigs). Contigs are often orders of magnitude longer than individual sequences, offering improved annotations, and key information...

Keywords: metagenomics

Reconstructing genomes from metagenomes: The holy grail of microbiology https://tess.elixir-europe.org/materials/reconstructing-genomes-from-metagenomes-the-holy-grail-of-microbiology-be78338f-13ef-40d6-92cf-621fbccf8808 Shotgun metagenomics provides insights into a larger context of naturally occurring microbial genomes when short reads are assembled into contiguous DNA segments (contigs). Contigs are often orders of magnitude longer than individual sequences, offering improved annotations, and key information about the organization of genes in cognate genomes. Several factors affect the assembly performance, and the feasibility of the assembly-based approaches varies across environments. However, increasing read lengths, novel experimental approaches, advances in computational tools and resources, and improvements in assembly algorithms and pipelines render the assembly-based metagenomic workflow more and more accessible. The utility of metagenomic assembly remarkably increases when contigs are organized into metagenome-assembled genomes (MAGs). Often-novel MAGs frequently provide deeper insights into bacterial lifestyles that would otherwise remain unknown as evidenced by recent discoveries. The increasing rate of the recovery of MAGs presents new opportunities to link environmental distribution patterns of microbial populations and their functional potential, and transforms the field of microbiology by providing a more complete understanding of the microbial life, ecology, and evolution. metagenomics 2016-12-16 2017-01-11