Deep sequencing
Summary
TLDRThis video from 'Somos Biology' concisely explains the concept of deep sequencing in genetics. It clarifies that deep sequencing isn't a specific method but a category based on the coverage and depth of sequencing a DNA fragment. The higher the read-through rate, indicating how many times a sequence is run, the more accurate the results. The video introduces the terms 'shallow' and 'ultra-deep' sequencing and explains the mathematical formula involving genome length, number of reads, and average read length to determine sequencing depth. It concludes by emphasizing that deep sequencing is about the number of times a sequence is read, not the technology used.
Takeaways
- ๐ฌ Deep sequencing is not a specific type of sequencing method like Sanger sequencing or Ion Torrent sequencing.
- ๐ Deep sequencing refers to the depth or coverage of sequencing, which depends on how many times a specific DNA fragment is sequenced.
- ๐ Coverage is the number of times a DNA fragment is run through the sequencer, and higher coverage leads to more accurate results with fewer errors.
- ๐ Running a sequence multiple times helps reduce errors in the sequencing data.
- ๐งฌ Deep sequencing occurs when a DNA fragment is sequenced more than seven times, whereas shallow sequencing involves fewer read-throughs.
- ๐ Ultra-deep sequencing involves running the same DNA fragment through the sequencer more than 100 times.
- ๐ข Three key parameters in deep sequencing are genome length, number of reads, and average read length.
- ๐งฎ The formula for calculating deep sequencing coverage is (Number of reads ร Average read length) / Genome length.
- ๐ป Most next-generation sequencing methods, like Illumina sequencing, typically involve deep sequencing due to the high number of read-throughs.
- ๐ฏ Deep sequencing is a categorization based on the extent of sequencing coverage, not a distinct technology or method.
Q & A
What is deep sequencing?
-Deep sequencing is a category of sequencing based on the depth or coverage of sequencing, which refers to the number of times a specific fragment of DNA is sequenced to ensure accuracy and minimize errors.
Why is deep sequencing necessary?
-Deep sequencing is necessary to achieve error-free results. Running the same DNA sequence multiple times helps to minimize errors and get more accurate data.
What is the difference between deep sequencing and other sequencing methods like Sanger sequencing or Ion Torrent sequencing?
-Deep sequencing is not a different type of sequencing method but a category that depends on the depth of sequencing. Sanger, Ion Torrent, and other methods can be used for deep sequencing if they are run multiple times to cover the DNA fragment extensively.
What is meant by 'coverage' in the context of sequencing?
-Coverage in sequencing refers to the number of times a specific length of DNA is sequenced. High coverage means the DNA fragment is sequenced many times to ensure accuracy.
What is the term used for sequencing a DNA fragment more than once or twice?
-The term used for sequencing a DNA fragment multiple times is 'read-through rate', which contributes to the overall coverage and depth of sequencing.
How is the depth of sequencing determined?
-The depth of sequencing is determined by the read-through rate, which is how many times the sequencer reads a specific length of DNA. More than seven times is considered deep sequencing, and more than a hundred times is ultra-deep sequencing.
What is the mathematical formula used to calculate the whole genome sequencing based on the script?
-The formula mentioned in the script is N multiplied by L by G, where N is the number of reads, L is the average read length, and G is the length of the genome.
What are the three parameters taken into account for whole genome sequencing according to the script?
-The three parameters are the length of the genome (G), the number of reads (N), and the average read length (L).
What is the significance of the number of reads (N) in sequencing?
-The number of reads (N) is significant because it determines the sequencing depth. Increasing this number increases the sequencing coverage, which is crucial for deep and ultra-deep sequencing.
Can the same sequencing technologies be used for both shallow and deep sequencing?
-Yes, the same sequencing technologies, such as Illumina sequencing or Ion Torrent sequencing, can be used for both shallow and deep sequencing. The difference lies in the number of times the sequencer reads the DNA fragment.
How does the script define 'ultra-deep sequencing'?
-According to the script, 'ultra-deep sequencing' is defined as sequencing the same DNA fragments more than a hundred times, providing an even higher level of coverage and accuracy.
Outlines
๐งฌ Deep Sequencing Explained
This paragraph introduces the concept of deep sequencing, distinguishing it from other sequencing methods like Sanger, Illumina, or Ion Torrent sequencing. It emphasizes that deep sequencing is a category of sequencing based on the depth or coverage of sequencing a specific DNA fragment. The paragraph explains that coverage is determined by the number of times a DNA fragment is sequenced to ensure error-free results. It also introduces the term 'read-through rate' and explains its importance in achieving high-quality sequencing data. The paragraph concludes with a brief mention of a mathematical formula involving genome length, number of reads, and average read length to calculate the sequencing depth.
Mindmap
Keywords
๐กDeep Sequencing
๐กCoverage
๐กRead-through Rate
๐กError Minimization
๐กShallow Sequencing
๐กUltra Deep Sequencing
๐กGenome Length
๐กNumber of Reads
๐กAverage Read Length
๐กSequencing Technologies
๐กSequencing Formula
Highlights
Deep sequencing is a category of sequencing based on depth or coverage, not a distinct method like Sanger or Ion Torrent sequencing.
Coverage is determined by the number of times a specific DNA fragment is sequenced.
High depth or coverage sequencing is achieved by sequencing the same DNA fragment multiple times to ensure accuracy.
Running a DNA sequence multiple times helps minimize errors and improve result accuracy.
The term 'read-through rate' refers to how many times a DNA sequence is loaded and sequenced.
Shallow sequencing involves reading a DNA fragment one to five times, whereas deep sequencing is more than seven times.
Ultra-deep sequencing involves sequencing the same DNA fragment hundreds of times.
A mathematical formula is used to calculate deep sequencing based on genome length, number of reads, and average read length.
The number of reads is a critical parameter in determining whether sequencing is deep or ultra-deep.
Illumina sequencing and other next-generation sequencing technologies can be classified as deep sequencing based on read-through rate.
Deep sequencing does not refer to a specific technology but rather the extent of sequencing coverage.
The video explains the concept of deep sequencing in a brief and accessible manner.
The importance of deep sequencing for obtaining error-free results is emphasized.
The video provides a clear distinction between shallow, deep, and ultra-deep sequencing.
Understanding the parameters of deep sequencing is crucial for accurate DNA analysis.
The video encourages viewers to subscribe and explore more sequencing videos for comprehensive knowledge.
Transcripts
come back friends welcome to another
video from somos biology in this video
I'm in a very brief manner I'm going to
talk about what is a deep sequencing
I've heard about confusion about the
deep sequencing first things deep
sequencing is not any other type of
sequencing methods like by the
sequencing or for five for sequencing or
Ion Torrent sequencing it's not it is a
category of sequencing depending upon
the depth of that sequencing or the
coverage of that sequencing okay now dip
and coverage of the sequencing is
counted based on how many number of
times you run the sequencing for a
specific fragment of the DNA a specific
length of the DNA okay let's say you
have a length of 200 base pair long and
you run this 200 base pair long DNA
third 300 times okay for a sequencing
that is known as the coverage it will be
huge or high depth for that sequencing
okay that is also known as the
read-through how many times you you load
that sequence and you want the sequencer
to give you the data now why we require
to run a same sequence multiple times
now it is important to understand error
free result because if you run a DNA
sequence for one or twice in that case
the data that you will get is not always
accurate
most of the cases it carries lot of
mistakes and errors but if you want to
get a better result you need to load
that DNA multiple times through the
sequencer you get multiple data from it
and then you get once you get all the
data together we'll combine the data to
get a proper data without or not
actually without but with less error so
to minimize error we run multiple times
for a specific length of the DNA we read
it multiple times that's called the
read-through rate okay and that is the
coverage so so the based on these two
parameters like depth and coverage we
measure some type of sequencing as a
shallow sequencing and some type of
sequencing as a deep sequencing solution
of sequencing means in those sequencing
you only take it for one
not two or less than five times the
sequencer is read through for each of
those lengths of the DNA but if it is
more than seven times if the sequencing
is read through more than seven times
that is known as a deep sequencing now
nowadays we also run the same sequence
data the same DNA fragments more than
even hundred times that is known as
ultra ultra deep sequencing okay so so
there is a formula mathematical formula
to understand about the whole process
and based on three different parameters
one is the length of the genome the big
how much big your genome is and it's
very easy second is the number of reads
that means how many times you want the
whole genome sequence to be sequenced by
the sequencer and third is the average
read length average read length means
the fraction of the DNA every time you
are running in the sequencer that length
of the DNA okay so the complete genome
and here is the fragment that is genome
that you are loading and getting the
data and this is how many times you're
loading it to get the data these are the
three different parameters that we take
account and the formula that we get is
in multiplied by L by G this is the
formula to calculate the whole thing in
multiplied by L by G the number of reads
that matters a lot if you increase this
number the sequencing number all also
increase and if it gets more than seven
X or seven times then you would call it
a deep sequencing if it gets more than
100 times it will it will be known as
ultra deep sequencing this is the idea
right so it's not any type of sequencing
approach this is just the way to
categorize the type of sequencing that
we are dealing with now you can run
Illumina sequencing a normally Illumina
sequencing and most of the next
generation sequencing like Illumina
sequencing or Ion Torrent sequencing we
run it more than seven times so we call
them deep sequencing also so the whole
process is known as deep sequencing and
that in the sequencer that we allow a
called deep sequencer but is
nothing extra about it the same
processes same technologies are used but
it depends on how many times you you go
through the read how many times the
sequencer read your sequence that is the
idea about the deep sequencing so I hope
you understand about the deep sequencing
if you liked the video please hit the
like button subscribe to my channel the
links are provided here in the top as
well as in the bottom and obviously if
you want to know more about the
sequencing you can watch all the
sequencing videos from my channel they
are all good and we hope they all will
help you so thank you very much
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