Yes and no. Paired end reads give you either longer reads or longer range information. The problem isn't fixed because as the technology gets better we just push up the read length.
Those algorithms, largely based on De Bruijn graph methods, are specifically designed to handle the short-read, high-coverage case. There's no reason to think that they will work well on the long-read low-coverage case.
You might be better off just BLASTing them together.
it's still inaccurate, maybe only in the ~90% accuracy rate (not a good thing when you're reading 3B base pairs)
Former de novo assembly software writer here. Do we have a good handle on the kinds of errors that you tend to find? You know how 454 reads tends to miscount repeat sequences and Illumina tends to decline in quality along the read. Do we understand where the errors come from?
Also, are the errors correlated? If you try to sequence the same 500k read twice, will it make errors in the same places?
That's what we do now with short reads. It kind of works, but only because we understand in a lot of detail about how errors happen.
For example, 454 sequencing tends to get the number of nucleotides in a repeat sequence wrong. So, for example, CTAAAGT might be read as CTAAAAGT. Illumina sequencing doesn't have that problem, but tends to degrade along the length of the read. So the last few nucleotides are more likely to be wrong than the first few.
And this is just read errors; with short-read sequencing, there are also PCR amplification errors, which is why we think nanopore sequencing will do better. When you start "unwinding" a chromosome, the parts that you unwind first tend to get amplified more than the parts that you unwind nearer to the end. Some sequences are amplified more than others for chemical reasons, and the relative error might depend on the specific revision of reagent chemicals.
We don't really understand enough about nanopore sequencing to be able to develop appropriate algorithms to match long-read sequences together. We don't even know what the right number of multiple passes is yet. And that's important, because genomics and transcriptonomics are important, but the bigger issue for researchers is economics.
I don't know if you knew this, but patent nonsense is also easily found via Google and other search engines. This is especially true of the Voynich manuscript. This is one reason why it is considered courteous for a person making an argument to give some pointers as to which information they believe supports that argument.
This is a random Internet comment section, so nobody expects a comprehensive literature review. But, you know, something.
I can also assure you that NOBODY is RUSHING to get these new fangled automobile thingies.
It took at least 60 years between the invention of the automobile to the time when there was around one automobile per family, and at least 80 years before an automobile was cost-effective for most families (i.e. it cost less than 10% of the median annual household income).
Even when you can see a clear advantage, that doesn't mean everyone is in a rush to get one.
Consciousness is obviously a thing, but the problem is that we only have one example (broadly construed) to go on. And when you only have one example of something, it's impossible to define.
It's kind of like how Pluto was a planet and then it wasn't. It was the discovery of more planet-like things that made us think harder about what constitutes a "planet".
My prediction, should they try this, is exactly what happened to video streaming services. They would make a modest amount of good quality music that, apart from one or two minor hits, essentially nobody will listen to because it's too niche or only those who use their particular service has a chance to hear it.
Apartheid was a social and legal policy of racial segregation. When it ended in 1994 it was pretty unusual for a modern western society. When it began in 1948, it wasn't terribly unusual.
Well, it wasn't unusual in the United States. It was highly unusual everywhere else with a few notable exceptions.
Most non-fascist old world European countries didn't really have racial segregation by this time. For the most part, it was subtle and largely cultural, not legal.
As for the new world, that largely depended on its history. Most South American countries had no such laws since the revolutions of the early 19th century; Brazil took pride in being a "racial democracy". Australia didn't really have race laws except for indigenous people (which is a story in itself). The general feeling among the racists of Australia is that aboriginality should be bred out. (Australia's racists have always been a bit more half-arsed than in most countries.)
So the way I see it, South Africa was introducing anti-miscegenation laws exactly at the time when everyone else had already, or were in the process of, phasing them out. Except for the US, pretty much everyone else thought they were archaic rather than traditional.
It's a reasonably standard English idiom, and extremely common in Slashdot writeups, to use constructions of this form: If [bad thing], or even if [fairly innocent thing], then [bad consequence either way].
Yes, my doctor told me during a house call, while I was getting a coal delivery. Now if you'll excuse me, I need to get some carbon paper for my typewriter.
Things don't fall neatly into current American polarised lines.
I'm not a conservative (my political beliefs are best described as "inconsistent"). Nonetheless, "conservativism" is the position that a strong unified society can be based around traditional values and institutions that are worth preserving.
There's nothing traditional about apartheid; even the few UK conservatives who secretly supported the regime only did so because they believed the world needed South Africa's help in fighting communism. Most conservative politicians in democratic countries outside of South Africa were against apartheid in principle.
Of all the stupidity that Python requires and encourages, significant whitespace is by far the least objectionable.
FORTRAN had significant whitespace. Occam had significant whitespace. Haskell has significant whitespace. Makefiles have significant tabs for Knuth's sake. We're grownups and we can cope.
The main problem with Python is literally everything else.
Slashdot Mirror
Yes and no. Paired end reads give you either longer reads or longer range information. The problem isn't fixed because as the technology gets better we just push up the read length.
Those algorithms, largely based on De Bruijn graph methods, are specifically designed to handle the short-read, high-coverage case. There's no reason to think that they will work well on the long-read low-coverage case.
You might be better off just BLASTing them together.
it's still inaccurate, maybe only in the ~90% accuracy rate (not a good thing when you're reading 3B base pairs)
Former de novo assembly software writer here. Do we have a good handle on the kinds of errors that you tend to find? You know how 454 reads tends to miscount repeat sequences and Illumina tends to decline in quality along the read. Do we understand where the errors come from?
Also, are the errors correlated? If you try to sequence the same 500k read twice, will it make errors in the same places?
String or nothing!
That's what we do now with short reads. It kind of works, but only because we understand in a lot of detail about how errors happen.
For example, 454 sequencing tends to get the number of nucleotides in a repeat sequence wrong. So, for example, CTAAAGT might be read as CTAAAAGT. Illumina sequencing doesn't have that problem, but tends to degrade along the length of the read. So the last few nucleotides are more likely to be wrong than the first few.
And this is just read errors; with short-read sequencing, there are also PCR amplification errors, which is why we think nanopore sequencing will do better. When you start "unwinding" a chromosome, the parts that you unwind first tend to get amplified more than the parts that you unwind nearer to the end. Some sequences are amplified more than others for chemical reasons, and the relative error might depend on the specific revision of reagent chemicals.
We don't really understand enough about nanopore sequencing to be able to develop appropriate algorithms to match long-read sequences together. We don't even know what the right number of multiple passes is yet. And that's important, because genomics and transcriptonomics are important, but the bigger issue for researchers is economics.
Not its own Slashdot, no. This is the closest.
The "useful idiot" pay scale doesn't give bonuses. Don't ask me how I know.
That's what they want you to think.
I don't know if you knew this, but patent nonsense is also easily found via Google and other search engines. This is especially true of the Voynich manuscript. This is one reason why it is considered courteous for a person making an argument to give some pointers as to which information they believe supports that argument.
This is a random Internet comment section, so nobody expects a comprehensive literature review. But, you know, something.
I can also assure you that NOBODY is RUSHING to get these new fangled automobile thingies.
It took at least 60 years between the invention of the automobile to the time when there was around one automobile per family, and at least 80 years before an automobile was cost-effective for most families (i.e. it cost less than 10% of the median annual household income).
Even when you can see a clear advantage, that doesn't mean everyone is in a rush to get one.
Thanks for telling Slashdotters that Cupertino is in the Silicon Valley. We had no idea.
That's for the dozen or so people who read the weekly Slashdot article which concerns Australia.
"Tipping a robot" sounds like something drunken MIT students would do.
That isn't quite what happened.
You may credit me as "some random person on Slashdot".
Consciousness is obviously a thing, but the problem is that we only have one example (broadly construed) to go on. And when you only have one example of something, it's impossible to define.
It's kind of like how Pluto was a planet and then it wasn't. It was the discovery of more planet-like things that made us think harder about what constitutes a "planet".
No need to be sorry. I didn't say "Republicans", and nor did the post I was responding to. I said "conservative politics".
No, C++ is not for you.
See also: Netflix, Hulu, Amazon...
My prediction, should they try this, is exactly what happened to video streaming services. They would make a modest amount of good quality music that, apart from one or two minor hits, essentially nobody will listen to because it's too niche or only those who use their particular service has a chance to hear it.
We aren't out of science, but on the other hand we are also not out of bongs to hit. While this is the case, questions like this will still be asked.
Apartheid was a social and legal policy of racial segregation. When it ended in 1994 it was pretty unusual for a modern western society. When it began in 1948, it wasn't terribly unusual.
Well, it wasn't unusual in the United States. It was highly unusual everywhere else with a few notable exceptions.
Most non-fascist old world European countries didn't really have racial segregation by this time. For the most part, it was subtle and largely cultural, not legal.
As for the new world, that largely depended on its history. Most South American countries had no such laws since the revolutions of the early 19th century; Brazil took pride in being a "racial democracy". Australia didn't really have race laws except for indigenous people (which is a story in itself). The general feeling among the racists of Australia is that aboriginality should be bred out. (Australia's racists have always been a bit more half-arsed than in most countries.)
So the way I see it, South Africa was introducing anti-miscegenation laws exactly at the time when everyone else had already, or were in the process of, phasing them out. Except for the US, pretty much everyone else thought they were archaic rather than traditional.
And in what programming language did those guys work at that time?
Mostly pre-ANSI C++. Smalltalk also gets quite a bit of coverage in GoF.
It's a reasonably standard English idiom, and extremely common in Slashdot writeups, to use constructions of this form: If [bad thing], or even if [fairly innocent thing], then [bad consequence either way].
Yes, my doctor told me during a house call, while I was getting a coal delivery. Now if you'll excuse me, I need to get some carbon paper for my typewriter.
Things don't fall neatly into current American polarised lines.
I'm not a conservative (my political beliefs are best described as "inconsistent"). Nonetheless, "conservativism" is the position that a strong unified society can be based around traditional values and institutions that are worth preserving.
There's nothing traditional about apartheid; even the few UK conservatives who secretly supported the regime only did so because they believed the world needed South Africa's help in fighting communism. Most conservative politicians in democratic countries outside of South Africa were against apartheid in principle.
Of all the stupidity that Python requires and encourages, significant whitespace is by far the least objectionable.
FORTRAN had significant whitespace. Occam had significant whitespace. Haskell has significant whitespace. Makefiles have significant tabs for Knuth's sake. We're grownups and we can cope.
The main problem with Python is literally everything else.