subject
Intro

Coursera: Algorithms for DNA Sequencing

 with  Ben Langmead and Jacob Pritt
Class Central Course Rank
#3 in Subjects > Data Science > Bioinformatics

We will learn computational methods -- algorithms and data structures -- for analyzing DNA sequencing data. We will learn a little about DNA, genomics, and how DNA sequencing is used. We will use Python to implement key algorithms and data structures and to analyze real genomes and DNA sequencing datasets.

Syllabus

DNA sequencing, strings and matching
This module we begin our exploration of algorithms for analyzing DNA sequencing data. We'll discuss DNA sequencing technology, its past and present, and how it works.

Preprocessing, indexing and approximate matching
In this module, we learn useful and flexible new algorithms for solving the exact and approximate matching problems. We'll start by learning Boyer-Moore, a fast and very widely used algorithm for exact matching

Edit distance, assembly, overlaps
This week we finish our discussion of read alignment by learning about algorithms that solve both the edit distance problem and related biosequence analysis problems, like global and local alignment.

Algorithms for assembly
In the last module we began our discussion of the assembly problem and we saw a couple basic principles behind it. In this module, we'll learn a few ways to solve the alignment problem.

17 Student
reviews
Cost Free Online Course (Audit)
Subject Bioinformatics
Provider Coursera
Language English
Certificates Paid Certificate Available
Hours 4-6 hours a week
Calendar 4 weeks long
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17 reviews for Coursera's Algorithms for DNA Sequencing

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1 out of 1 people found the following review useful
2 years ago
Mark Wang completed this course, spending 5 hours a week on it and found the course difficulty to be medium.
Hello! I am a developer who's considering moving into bioinformatics. I took the course to get an understanding of the type of problems that computer scientists face in bio. Wanted to give you some feedback. Pros 1:) Good introduction to the problems faced by computer scientists in bioinformatics. Got me very interes Read More
Hello! I am a developer who's considering moving into bioinformatics. I took the course to get an understanding of the type of problems that computer scientists face in bio. Wanted to give you some feedback.

Pros

1:) Good introduction to the problems faced by computer scientists in bioinformatics. Got me very interested in the topic.

2:) Described the right amount of biology: enough to understand problem, but definitely geared towards algorithm side.

3:) Actual description of the algorithms and their complexity was pretty clear.

4:) Practical slant with lots of actual coding.

5:) Pace was good and Ben is talented an explaining concepts.

Cons

1:) Would have been nice to use some of the tools bioinformaticians use. I understand that we're learning from first principle a lot of the algorithms that they actually use in their tools, but it would have been nice to learn, say "Boyer Moore is used in such and such tools whereas kmer indexing is used in such and such" and then actually tried them out.

2:) Along with that, if we had a meatier project than just the programming assignments we were given, one closer to what actual bioinformaticians do, that would also have bee nice.

Of course, both of those cons are perhaps outside the scope of the class, so I understand why they weren't included. Overall, very worthwhile class, 4.5 stars out of 5 (rounding up to 5).
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1 out of 2 people found the following review useful
2 years ago
Daria completed this course.
This course deals with the algorithms employed by mapping and genome assembly programs commonly used. It was only after completing the course that I realised that the course instructor, Ben Langmead, is actually the first author of the bowtie paper which is one of the most commonly used programs for DNA mapping. The le Read More
This course deals with the algorithms employed by mapping and genome assembly programs commonly used. It was only after completing the course that I realised that the course instructor, Ben Langmead, is actually the first author of the bowtie paper which is one of the most commonly used programs for DNA mapping. The lecture material is extremely well explained and accessible both to students with a computational background and to biologists. The algorithms employed are much better explained than in some other bioinformatics courses on Coursera that deal with some similar topic (UCSD Specialisation, etc) as the course specifically deals with the algorithms rather than teaching bioinformatics in general (though I find the other courses quite good too). The Practical courses are extremely useful, and help a great deal to understand how the algorithms described during the lectures can be easily applied in an accessible programming language. The Practicals are carried out in Python. Prior knowledge of Python is definitely a very big plus to getting the most out of this course, but not essential to understanding. I really recommend this course and really hope to see more courses from the same instructor in the future!
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1 out of 1 people found the following review useful
2 years ago
Dejan Đukić completed this course.
I feel that I have been finally introduced to the real world problems, their potential solutions and the paths for the improvement of such solutions. I feel that I've learned a lot about implementing the knowledge I've acquired so far and not only the knowledge gained through the specialization courses I've completed, Read More
I feel that I have been finally introduced to the real world problems, their potential solutions and the paths for the improvement of such solutions. I feel that I've learned a lot about implementing the knowledge I've acquired so far and not only the knowledge gained through the specialization courses I've completed, and, more importantly, I feel myself much more drawn to the field of computational molecular biology and genomics than I ever was before. The only thing the course is missing is more of the same. I highly recommend the course for anyone interested in making first steps in serious DNA analysis and processing. Dr. Ben Langmead, along with lecturer Jacob Pritt, has done a magnificent job at making this course engaging, progressive and fun.

My background is predominantly in genetics and molecular biology. I also had relevant programming experience in Python and would recommend anyone who plan on taking the course to acquire the same. Any other programming language would probably be fine but the language of choice for the course is Python.

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2 out of 2 people found the following review useful
2 years ago
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Leif Ulstrup completed this course, spending 6 hours a week on it and found the course difficulty to be medium.
I have taken six other courses in this JHU Genomics series on Coursera and many others in Data Science @ JHU, Cybersecurity @ the U of Maryland etc on Coursera. I think this module is one of the very best I have taken. The video lectures with theory, explanations, and the implementation practicals are excellent. Just t Read More
I have taken six other courses in this JHU Genomics series on Coursera and many others in Data Science @ JHU, Cybersecurity @ the U of Maryland etc on Coursera. I think this module is one of the very best I have taken. The video lectures with theory, explanations, and the implementation practicals are excellent. Just the right length lecture modules with crisp explanations and examples. The Quiz and Programming HW assignment content and approach reinforces making sure one understands the key concepts. The learning/frustration quotient on this class is very high. The Python HW programming assignments have all been challenging and fun. The final one is terrific and getting the virus back from BLAST was a blast - giving one a taste of the excitement of scientific discovery.
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1 out of 2 people found the following review useful
2 years ago
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Tyler Devlin completed this course.
A solid course from a great instructor. Unlike some of the other courses in the Genomic Data Science Specialization, which have been shallow or poorly taught, this course is challenging (but not undoable) and the lectures are very well organized.

The course is short, so you should not expect to get a full introduction to the field. But for its length, the course delivers a lot.
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1 out of 2 people found the following review useful
2 years ago
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Anonymous completed this course.
Good course for all levels. Not much previous experience needed and a good learning curve. Recommended for people of all backgrounds who want to learn how sequencing works.
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2 years ago
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Allison Cooper completed this course, spending 4 hours a week on it and found the course difficulty to be medium.
This was a very nice course. The instructor explained things really well and the problem sets were fun, interesting, challenging enough to be motivating but doable. I had taken the San Diego bioinformatics courses, and this course helped me solidify some of the material that flew by in that other course. Highly recommended!
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2 years ago
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Anonymous completed this course.
This course was organized excellently. For a course with a duration of just 4 weeks it covers an amazing amount of required DNA sequencing background material and algorithms. Lectures were great and practicals were amazing since they covered coding of algorithms. Course offers plenty of scope for future learning.
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11 months ago
Chrys completed this course.
Really good course. Compared to the other courses in the specialisation this one is really awesome and helpful. The other python course does not prepare you for the level of this course because it gets quite tricky , quite fast but stick with it. The instructors are amazing and really cool.
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2 years ago
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Anonymous completed this course.
I found the lectures and the assignments to be very helpful and interesting. The course also provided an excuse to learn some of the Python programming language, which I encounter from time to time in my current career.
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2 years ago
Alexander Glukhovtsev completed this course, spending 16 hours a week on it and found the course difficulty to be medium.
Great course.

Thanks to wonderful instructors:

Ben Langmead, PhD and Jacob Pritt.

Highly recommended to all interested in algorithms design in general, applied computer science and modern bioinformatics.
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2 years ago
Colin Khein completed this course and found the course difficulty to be medium.
This was the high point of an otherwise dreadful specialization. It was well-taught. And both the exercises & tutorial format were well-suited to the course.
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1 out of 2 people found the following review useful
2 years ago
Radu Dragusin completed this course.
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0 out of 5 people found the following review useful
2 years ago
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Anonymous is taking this course right now.
This course has a serious problem for anyone who has only taken the previous Introduction to Python course. This course fails to cover how to install and use the Python IDE (e.g. Anaconda, Jupyter, Notebook). The instructors just go ahead and present material in Notebook without showing how to load it, creating, or edi Read More
This course has a serious problem for anyone who has only taken the previous Introduction to Python course. This course fails to cover how to install and use the Python IDE (e.g. Anaconda, Jupyter, Notebook). The instructors just go ahead and present material in Notebook without showing how to load it, creating, or edit it. They were unable to explain the errors and grayed-out controls that I asked them about. They are unresponsive to questions. Answers were often variations on "you're really close" which is pointless. They do not seem to know how they got their own tools set up and now are unable to state a simple series of steps and configuration settings. Consequently, I come away feeling that the Python language and tool suite is not suitable for real-world work. It is a patchy academic introductory teaching tool at best.
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1 out of 4 people found the following review useful
2 years ago
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Anonymous partially completed this course.
As any course in both "specializations" from Johns Hopkins, this is a just a random collection of things with no structure. Don't waste your time, you will not learn much.
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2 years ago
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Anonymous completed this course.
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2 years ago
Chema Cortés completed this course.
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