Struggling with writing your metagenomics thesis? You're not alone.

Crafting a comprehensive and

Navigating through vast amounts of scientific literature, designing experiments, and analyzing data
can be overwhelming, especially when coupled with the pressure of meeting deadlines and adhering
to academic standards. Many students find themselves grappling with writer's block, uncertainty
about their findings, or struggling to articulate their ideas effectively.

Fortunately, there's a solution to alleviate some of this burden: seeking assistance from professionals.
⇒ HelpWriting.net ⇔ offers expert thesis writing services specifically tailored to meet the unique
needs of students in the field of metagenomics. Our team of experienced writers and researchers
possesses the expertise and skills necessary to help you produce a high-quality thesis that meets the
rigorous standards of academia.

By entrusting your thesis to ⇒ HelpWriting.net ⇔, you can:

1. Save Time: Focus on other aspects of your research while our experts handle the writing
process.
2. Ensure Accuracy: Benefit from our team's in-depth knowledge of metagenomics and their
commitment to precision and thoroughness.
3. Improve Clarity: Receive assistance in articulating your ideas clearly and coherently to ensure
maximum impact.
4. Meet Deadlines: Rest assured that your thesis will be delivered on time, allowing you to
meet academic deadlines without stress.

Don't let the challenges of thesis writing hold you back from achieving your academic goals. Visit ⇒
HelpWriting.net ⇔ today and take the first step towards completing your metagenomics thesis with
confidence.
These nutrients support large and diverse microbial communities, many of which provide direct
benefit to the plant. In essence, their goal was to collect large fragments from picoplankton genomic
DNA in an attempt to extract the genomic DNA from Crenarchaeota. Next, the DNA was digested
using restriction enzymes to achieve smaller fragments and then cloned into the Fosmid vector
library. I would argue that most knowledge about microbiology could not be discovered a priori. As
mentioned above, anvi’o tutorials, like this one for phylogenomics or this one for pangenomics, are a
great place to start. Meaning, Sample B seems to have the highest coverage for these contigs, but
evenly across, and Sample C seems to have the lowest, but again consistent within that sample. The
manuscript provided a breadth of reasoning and evidence for the utility of 16S rRNA gene as a
phylogenetic marker in biology, as well as a source of wisdom and outlook on the field of
microbiology. But the most impactful dichotomization of taxonomy came from the introduction of
Prokaryote-Eukaryote distinction by Edouard Chatton ( Sapp 2005 ). This method is being utilized
today to detect inter-strain variation ( Maistrenko et al. 2020; Van Rossum et al. 2020 ) as well as
detect regions of horizontal gene transfer and genomic islands ( Bazin et al. 2020 ). Additionally,
pangenomics can highlight disconnects between genomes who may look related phylogenomically
(based on single-copy core genes) but in terms of gene content are quite different ( Delmont and
Eren 2018 ). However, the first time GC content from nucleotide composition was used to examine
bacterial taxonomy was by ( Russell et al. 1973 ) (Figure 1). They are being more frequently referred
to as “metagenome-assembled genomes”, or MAGs, to better convey this. So let’s take a look at it
with ls, and then change into the “working” directory (which should be empty right now). All of
these discoveries would not have been possible without the integration of evolution (pangenomics)
and ecological (metagenomics) approaches. Specifically, scientists leveraged nucleotide content to
develop classifiers to predict the genome of origin of short oligonucleotide sequences ( Sandberg et
al. 2001; Abe et al. 2003 ). This method sounds very similar to the idea of grouping short
metagenomic contigs together into a bin. It would be the same as if we typed out each line in the file
with a space in between them. The Institute acts under the responsibility given to the National
Academy of Sciences by its congressional charter to be an adviser to the federal government and,
upon its own initiative, to identify issues of medical care, research, and education. Cultured
representatives could not keep up with the discovery of new phylotypes observed in the
environment. Here we are going to use it to visualize our metagenome and coverage from each
sample, to help us see how recovering “genomes” from metagenomes works. This left a significant
knowledge gap in terms of the function potential of these enigmatic diazotrophs and how they
impact biogeochemistry. Metagenomic studies have revealed that each person carries a unique
microbial community in his. In 2003, Craig Venter led the Global Ocean Sampling Expedition
(GOS), circumnavigating the. To address this data analysis challenge there were numerous data
analysis innovations in comparative metagenomics from clustering orthologs ( Yooseph et al. 2007 )
to gene catalogues ( Turnbaugh et al. 2007 ). Yet as Katherine McMahon puts it, “Genes are
expressed within cells, not in a homogenized cytoplasmic soup.” ( McMahon 2015 ) In other words,
the first comparative metagenomics projects were genome agnostic. Try to find the cluster of contigs
that represents Trichodesmium. To me, metagenomics is an amazing hypothesis generator and at this
point in this review I wanted to highlight some discoveries that were made possible from genome-
resolved metagenomics. Anne’s aesthetic intuition and visual acuity shaped the report as well as its
derivative materials. The specific areas as well as the tools used are highlighted for identifying
diversity, searching for novel genes and gene products, and investigating relationships among genes,
mRNAs, and proteins in microbial communities. This means that functional analysis necessitates the
transcription and translation of a particular gene and then ensuring that the product is secreted if it is
usually found on the outside of the cell. They change hazardous chemicals into forms that are less
caustic to both the people and the environment. Here’s a general overview of how we currently
recover m etagenome- a ssembled g enomes from metagenomes. This is a highly debated topic where
other groups have claimed there are still 3 branches ( Da Cunha et al. 2017 ). These analyses were
only possible through putting contigs in a genomic context through binning which allowed for a
phylogenomic approach to place these undiscovered genomes on a provocative branch of the tree of
life.
Here we are going to use it to visualize our metagenome and coverage from each sample, to help us
see how recovering “genomes” from metagenomes works. Anvi’o happens to have one, so we’re just
going to use that here. Studies showed that methyl parathion (MP) is generally hydrolyzable and
rapidly breaks down in water and sediments via photolysis and biodegradation by various
microorganisms. This study uses metagenomics to compare the effect of MP on farmland soil
microorganisms population. I would argue that motivation for a decade-long enrichment experiment
would have dwindled if it were not for discoveries such as ( Spang et al. 2015 ). Tyson et al. 2004
also took huge philosophical steps forward in defining the completeness of genomes recovered from
metagenomes. Fragments that did not contain a part of the Crenarchaeota ribosomal subunit were
not further sequenced. Functioning in accordance with general policies determined by the Academy,
the Council has become the principal operating agency of both the National Academy of Sciences
and the National Academy of Engineering in providing services to the government, the public, and
the scientific and engineering communities. It could depend on many factors (e.g. variation between
the samples, diversity of the communities, the assembler(s) you’re trying, you’re overall questions,
who knows how many others things?, etc.), and there can be datasets where a co-assembly would
give you a poorer output assembly than an individual assembly would. This manuscript looks to
further culture-independent microbial ecology by investigating the marine Archaea clade,
Creanrchaeota. Instead, they extracted large fragments of genomic DNA (up to 40 Kb) from
seawater and sequence via a Fosmid cloning approach. (See Box 3). That’s not to say all are
magically equally good in every sense, but most that gather a following will out-perform all others
under certain conditions. The clones were then screened for specifically archaeal DNA fragments by
amplifying 16S rRNA genes content from the fragments. The purpose of metagenomics is to collect
information regarding the physiology and genetics of uncultured organisms. The first examples of
tetranucleotide usage I could find was in 1984 to investigate methylation sites on post replicative
methylation of adenine in E. The rapid advancements in metagenomics are largely due to the
technical and analytical methods developed from high throughput platforms for cloning, DNA
sequencing, robotics, high-density microarrays, 2D-gel electrophoresis, and mass spectrometry as
well as associated bioinformatics softwares. If there was another phylogenetic marker of Archaea
more related to metabolism, there could have been a chance to explore a more novel genomic
neighborhood away from the 16S region. At its third meeting, on July 27, 2006, the committee was
briefed by: David J. This method is being utilized today to detect inter-strain variation ( Maistrenko
et al. 2020; Van Rossum et al. 2020 ) as well as detect regions of horizontal gene transfer and
genomic islands ( Bazin et al. 2020 ). Additionally, pangenomics can highlight disconnects between
genomes who may look related phylogenomically (based on single-copy core genes) but in terms of
gene content are quite different ( Delmont and Eren 2018 ). How does this hold up to today’s
standards for MAG completeness, redundancy, and contamination? (see Box 6). Our “capacity” to
sequence genes drastically changed our understanding of diversity and protein evolution. This
includes sequences such as 16S rRNA and rec A. This volume is recommended for scientists in any
field. If you “right” click on one of the specific contigs, you’ll get a menu where you can select
“Inspect”. For example, in BGC research, you had to use 16S amplicon sequencing to see if potential
microbes of interest (e.g. actinomycetes) were in a specific environment, then hope they could grow
in standard culture techniques and be screened for specific phenotypes. The nature of the data
demands that new methods in bioinformatics develop in order to identify organisms by their
genomes. We will focus in particular on how metagenomics affects concepts of organism and living
entity, and the connections between the older notion of superorganism and the emerging one of
metaorganism. This left a significant knowledge gap in terms of the function potential of these
enigmatic diazotrophs and how they impact biogeochemistry. Moreover, by providing direct access
to the pool of environmental genomes without the bias of cultivation, metagenomics offers the
possibility to explore the vast diversity of degradation pathways of environmental microorganisms,
which remain to a large extent poorly characterized (if not totally unknown). Woese has a few epic
quotes in this section that would be a injustice to paraphrase and are worth discussing more in-depth.
Differences will be noted where needed if working with a newer version, and there is a stellar, up-
to-date anvio metagenomics tutorial here.
By “walking” upstream and downstream from the phylogenetic marker, they hoped to obtain
physiological insights. This makes sense considering how labor intensive and expensive this
sequencing must have been at the time. Whether you’d want to do this normally or not is up to the
researcher, but that is roughly the average size of a bacterial gene, and the smaller contigs become
the more difficult it becomes to get useful information out of them. Register for a free account to
start saving and receiving special member only perks. Dr. Harvey V. Fineberg is president of the
Institute of Medicine. Since the field of metagenomics rests on the technology of Next-Generation
sequencing and Long-read sequencing, I was inspired to review origins of a few fundamental
microbiology technologies. For example, in BGC research, you had to use 16S amplicon sequencing
to see if potential microbes of interest (e.g. actinomycetes) were in a specific environment, then hope
they could grow in standard culture techniques and be screened for specific phenotypes. In this
chapter, we cover primary raw nucleotide sequencing data repositories, the annotated nucleotide
sequence databases and the management of protein information from metagenomics studies, taking
as example resources the European Nucleotide Archive and the UniProt Universal Protein Resource.
Natural product discovery via BGC research at this point had been driven by microbial isolation with
selective media to search for specific antibiotic and metabolic phenotypes. J. Handelsman et al. 1998
recognized how using an entire sample’s worth of DNA could be beneficial for accessing novel BGC
loci (similar to how Stein et al. 1996 wanted to explore novel metabolisms in Archaea described
below). With massive publicly available MAG datasets, large meta-analyses can be performed and
questions relating to global prevalence of bacterial taxa or proteins can be achieved. The many
hurdles that are faced with the assembling of metagenomic sequences occur essentially from the
short reads and the high species difficulty of the population. Although within strain variation of
bacteria has been explored since the first MAGs were binned ( Simmons et al. 2008 ), the excess of
genomic data we now have at our disposal will allow us to address not only high resolution strain
variation questions but broad questions about the total sequence variability and gene content within
large phylogenetic groups. Tyson et al. 2004 defined “completeness” of their bins accounting the
amount of transfer RNA synthetases each genomic bin had. The broad field may also be referred to
as environmental genomics, ecogenomics or community genomics. Click here to buy this book in
print or download it as a free PDF, if available. Nevertheless, metagenomic sequences have particular
characteristics that are not especially appropriate for the study of HGT, mainly their short length and
their unknown origin. Koch’s assistant, Julius Richard Petri, expanded on Koch’s potato slices and
invented, you guessed it, the Petri dish. Appointed by the National Research Council, he was
responsible for making certain that an independent examination of this report was carried out in
accordance with institutional procedures and that all review comments were carefully considered.
Within microbial communities, the archaeas harbour an excellent repertoire of novel genes for
biotechnological applications and represent a key step for understanding evolution and to
comprehend metabolic pathways. Despite this, there are still some steps that would take a bit too
long to just wait for, so in those cases there will be examples of how the code would be run, but
we’ll just pull result files from a subdirectory that comes with the data download so skip some of the
more time-consuming steps. On the other hand, individual (short) reads will be investigated directly
against records of known genes to recognize homologous development. Reveillaud et al. 2019 found
novel viral diversity in Wolbachia MAGs from insect ovaries via differential gene-cluster read
recruitment. These could represent house-keeping genes and functions that are related to the central
dogma. We also thank Anne Jurkowski for her dedication to this report and its authors. Finally, there
were examples of the entire 16S-23S operons found on fosmids. Let’s take a look back and explore
the evolution of kmers and genomes. This method is most useful when studying genomic fragments
within a taxon. The ultimate approach may not be very specific or sensitive in recognizing the
homologous sequences, which may additional prejudice the successive collection analysis. The deep-
sea tube worm, Riftia pachyptila, and a bacterium (Boetius, 2005). Anvi’o happens to have one, so
we’re just going to use that here.
While metagenomics takes advantage of this existing paradigm, new methods and concepts are also
required to rise to the many novel challenges presented by metagenomic data. The operation within
the parentheses here will be performed and the output of that replaces the whole thing. A duplication
of an SCGs would infer that a contig from another population was included into the MAG by
mistake since by definition each SCG should only occur once. Here we are working with 4 samples
from an enrichment culture, and the communities should be pretty well constrained - certainly
relative to complex environmental samples like, say, a transect across soil. On the other hand,
metagenomic read recruitment allows one to ask ecological questions about the detection of specific
microbes across samples. We now have the opportunity to explore the interactions between plants
and microbes through cultivation independent study of the microbial communities. There are good
instructions at the anvi’o tutorial for importing taxonomy, and here are the commands that were used
to generate what’s in our results file. It is commonly applied as a dust, powder, concentrate,
emulsion, or granules to inhibit boll weevils and other insects found in agricultural crops. Moreover,
accessory genes that consistently recruit reads from metagenomes could infer that there is a culturing
bias and the genomes available do not represent ecological relevant population functional capacity.
Home Electronic Theses and Dissertations (2010 - Present) Published ETD Collection Comparative
Metagenomics To Study The Impact Of Methyl Parathion On Farmland Bacterial Populations. Three
major benefits of co-assembly include: 1) higher read depth (this can allow you to have a more robust
assembly that captures more of the diversity in your system, but not always ); 2) it facilitates the
comparison across samples by giving you one reference assembly to use for all; and 3) it can
substantially improve your ability to recover genomes from metagenomes due to the awesome power
of differential coverage (see summary image above). The special words of the loop are for, in, do,
and done. By doing so, we can observe the varying degrees of diversity of organisms among
different samples. The integration of microbial community structure with function, taking into
account uncultured microbes in diverse environments, remains particularly challenging. Binning
algorithms can add contigs to bins that in reality do not belong to the population genome. Woese
reflects on this theory and how it may have also shaped our perception of Prokaryotes. Once the
sequences are identified, the functions of the fragments can be determined. As the amount and types
of anchors increase, the utility of sequenced-based analysis will also increase since it relies on
phylogenetic markers to identify the organism of origin. This is currently the most powerful tool we
have for attempting to recover genomes from metagenomes. Due to this culturing bias it became
hard to extrapolate metabolic capabilities and phenotypes of cultured representatives to newly
discovered sequence phylotypes; more genomic context was needed. This technological leap is
responsible for the “Golden Age of Bacteriology’’ and an exponential increase in our knowledge of
microbial diversity and function leading to discoveries such as antibiotics. The field has broad
implications for human health and disease, animal production and environmental health. Maybe
metagenomics was not the best word to describe our field. The impact of metagenomics is witnessed
in the development of commodity and fine chemicals, agrochemicals and pharmaceuticals where the
benefit of enzyme-catalyzed chiral synthesis is increasingly recognized. This is because spaces are
important to the command-line’s interpretation, whereas commas don’t interfere with how it is
interpreting the command and the information gets to megahit successfully. As Next-Generation
deep sequencing became more affordable, sequencing depth of metagenomics projects increased.
This step takes having a database setup and takes some time to run. This manuscript looks to further
culture-independent microbial ecology by investigating the marine Archaea clade, Creanrchaeota.
The product reflects both Ann’s attention to our charge and her ability to provoke us into addressing
it thoroughly. By putting contigs with nitrogen fixing genes into genomic context, we can now create
targeted culturing campaigns to isolate these novel diazotrophs.
Other Bacterial phyla such Proteobacteria and Firmicutes have been linked to nitrogen fixation via
PCR amplicon studies of the nifH gene. Metagenomics has taken off as one of the major cutting-
edge fields of research. We will focus in particular on how metagenomics affects concepts of
organism and living entity, and the connections between the older notion of superorganism and the
emerging one of metaorganism. Today we refer to nucleotide content in the context of metagenomics
as k-mer content but Tyson et al. 2004 used GC content (i.e. a combination of Guanine and Cytosine
1-mers). This has allowed for the creation of higher quality MAGs due to the emergence of coverage
senstivitive algorithms for binning. Increased understanding of how microbial communities cope
with pollutants could help to assess the potential of contaminated sites to recover from pollution and
increase the chances of bioaugmentation or biostimulation trials to succeed. The specific areas as
well as the tools used are highlighted for identifying diversity, searching for novel genes and gene
products, and investigating relationships among genes, mRNAs, and proteins in microbial
communities. Fortunately, the microbial community can take care of this crisis. For example, one
could investigate if a microbial population is a generalist (found in a lot of samples) or specialist
(found in a few samples often in high abundance) by looking at the distribution of detection across a
transect of the ocean. Once that loads up, click the “Draw” button at the bottom left and you should
see the metagenome appear. In the letter, Darwin comments on the results of an experiment
challenging Louis Pasteur’s interpretation of Spontaneous Generation (the belief that life
spontaneously arose from abiotic materials - an explanation for putrefying food) ( Madigan et al.
2018 ). Darwin’s description of the origin of life was in response to the Golden Age of Microbiology
and all of the creative theories of the time to explain microbial life. This is essentially accessing one
genome at a time. We also thank Anne Jurkowski for her dedication to this report and its authors.
Responsibility for the final content of the report rests entirely with the author committee and the
institution. It seems like everyday the microbiome is being implicated in a new health or geologic
process. It’s best to put anvio in it’s own environment, so we’ll just install bowtie2 and megahit first
with Conda. In the case of Prokaryotic vs Eukaryotic complexity I think the majority of arguments
highlight the complexity of organelles and genetic regulation that Eukaryotes have. To address this
data analysis challenge there were numerous data analysis innovations in comparative metagenomics
from clustering orthologs ( Yooseph et al. 2007 ) to gene catalogues ( Turnbaugh et al. 2007 ). Yet as
Katherine McMahon puts it, “Genes are expressed within cells, not in a homogenized cytoplasmic
soup.” ( McMahon 2015 ) In other words, the first comparative metagenomics projects were genome
agnostic. How does this hold up to today’s standards for MAG completeness, redundancy, and
contamination? (see Box 6). Gene-clusters that contain genes from which every genome has at least
one copy represent core functions of the microbes being compared. What other technological
innovations have pushed microbiology forward. While high-throughput DNA sequence analysis will
be an important tool for these studies, the immense richness and diversity of such communities
present a strong mandate for the use of functional metagenomics strategies that involve a broad
variety of screening methodologies to discover and study the currently unknown key biological
processes. Yet, as the century went on it became clear that culturing techniques were not keeping up
with the immense diversity of microbes. It is autonomous in its administration and in the selection of
its members, sharing with the National Academy of Sciences the responsibility for advising the
federal government. Leveraging metagenomic sequencing of large genomic fragments, Stein et al.
1996 could use “genomic walking” (looking upstream and downstream on genomic fragments from a
phylogenetic marker) in the marine environment. Recovery of metabolic pathways and gene clusters
involved in biosynthesis of antibiotics and bioactive molecules has increased the prospect of
identifying useful natural and synthetic products for drug development. It was only with the
development of high-throughput technology to analyze and sequence DNA from the natural
environment that information began to accumulate that demonstrated the exceptional diversity of
microbes in Nature - in fact, most microbes are entirely novel and have not previously been
described. Briefly, this theory proposes that life occurred in primitive anaerobic oceans and the first
organisms were “extreme heterotrophs” that assimilated already available, abiotically formed amino
acids and nucleotides. The ecological question in this paper was what is the functional potential of
the individual microbial community members in a low diversity biofilm found in an acid mine
drainage (pH 0.83)? Understanding life in extreme environments is important for fundamental
questions in regards to astrobiology and geobiology. The first examples of tetranucleotide usage I
could find was in 1984 to investigate methylation sites on post replicative methylation of adenine in
E.
Robert Koch is credited for developing the first microbial isolation techniques. The deep-sea tube
worm, Riftia pachyptila, and a bacterium (Boetius, 2005). In the letter, Darwin comments on the
results of an experiment challenging Louis Pasteur’s interpretation of Spontaneous Generation (the
belief that life spontaneously arose from abiotic materials - an explanation for putrefying food) (
Madigan et al. 2018 ). Darwin’s description of the origin of life was in response to the Golden Age
of Microbiology and all of the creative theories of the time to explain microbial life. The field of
metagenomics continues to evolve with large common datasets available to the scientific community.
This can be problematic for some tools, and it’s better to have simplified headers if you can.
Additionally, significant steps have been taken to expand our knowledge of the human gut
microbiome due to its correlation with health and disease ( Almeida et al. 2019; Pasolli et al. 2019 ).
Pasolli et al. 2019 highlighted how different non-western gut microbiomes are from western
microbiomes and how significantly undersampled they are. Upon the authority of the charter granted
to it by the Congress in 1863, the Academy has a mandate that requires it to advise the federal
government on scientific and technical matters. It's a quantum leap beyond traditional research
techniques that rely on studying—one at a time—the few microbes that can be grown in the
laboratory. This can be done by using nitrate for energy and by altering the gasoline until it contains
only an assortment of carbon dioxide and water. Tyson et al. 2004 also took huge philosophical steps
forward in defining the completeness of genomes recovered from metagenomes. In addition to
generating fundamental questions about biological ontology, metagenomics is leading a
transformation of standard life-science epistemology into multi-level systems-based understanding.
Initial sequencing initiatives for this program are in place and include metagenomic sequencing to
characterize the microbial communities from 15-18 body sites from at least 250 individuals. At its
third meeting, on July 27, 2006, the committee was briefed by: David J. Most of what we know
about these complex community interactions has been derived through study of organisms in pure
culture, but it is well known that the vast majority of microbes have not been cultivated. However,
sequenced-based analysis has its limitations as well. The field has broad implications for human
health and disease, animal production and environmental health. MTP-10005, an
alphaproteobacterium, since it is the one that has the biodegradation capability via the maleylacetate
and hydroxyquinol of the methyl parathion degradation pathway. This is a highly debated topic
where other groups have claimed there are still 3 branches ( Da Cunha et al. 2017 ). These analyses
were only possible through putting contigs in a genomic context through binning which allowed for
a phylogenomic approach to place these undiscovered genomes on a provocative branch of the tree
of life. Topics include: Conceptual frameworks, tools and methods, integration of complementary
approaches, horizontal gene transfer, analysis of complex microbial communities, public data
resources, plant-microbe interactions, bioremediation, industrial bioproducts, archaeal metagenomics,
bioprospecting novel genes, the human microbiome, and philosophical themes in metagenomics. Yet,
as the century went on it became clear that culturing techniques were not keeping up with the
immense diversity of microbes. But the most impactful dichotomization of taxonomy came from the
introduction of Prokaryote-Eukaryote distinction by Edouard Chatton ( Sapp 2005 ). This broad
understanding of the microbial tree of life will allow scientists to elucidate evolutionary questions
like never before. Yet in the context of metabolism, bacteria can access multiple terminal electron
acceptors to generate ATP when the majority of Eukaryotes can only utilize Oxygen - who’s complex
now. It is a very powerful tool used to determine linkage of traits, the organization of an organism's
genome, horizontal gene transfer, and distribution and redundancy of functions in a community. On
the other hand, individual (short) reads will be investigated directly against records of known genes
to recognize homologous development. For each sample layer, the visualization is showing the read
coverage for that sample to each contig as you travel around the circle. This is currently the most
powerful tool we have for attempting to recover genomes from metagenomes. Also, you can type in
a page number and press Enter to go directly to that page in the book. With a more effective analysis
approach, fragments that previously remained unidentified can be matched to their respective
organism, leading to an eventual completion of a reconstructed genome for that organism. Three
major benefits of co-assembly include: 1) higher read depth (this can allow you to have a more robust
assembly that captures more of the diversity in your system, but not always ); 2) it facilitates the
comparison across samples by giving you one reference assembly to use for all; and 3) it can
substantially improve your ability to recover genomes from metagenomes due to the awesome power
of differential coverage (see summary image above).