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Full courses online
 Algorithms for DNA Sequencing
 Full course on Coursera
 Lectures on YouTube (55 lectures, about 7 minutes each)
 Lecture notes on GitHub
 Practical IPython/Jupyter notebooks on GitHub
Recorded lectures
 Suffix tries and suffix trees
 BurrowsWheeler Transform
 FM Index
 RNAseq and cloud computing (BIRS, 3/30/17)
Lecture notes and IPython/Jupyter notebooks
 Introductory
 Strings and matching
 Strings and exact matching
 Notebook: Strings in Python
 Notebook: Naive exact matching
 BoyerMoore
 Notebook: Z algorithm
 Notebook: BoyerMoore
 Approximate matching
 Notebook: Naive approximate matching
 Notebook: Pigeonhole principle
 Strings and exact matching
 Indexing
 Indexing with substrings
 Notebook: Hash table substring index
 Notebook: Grouped and ordered indexes
 Tries and suffix tries
 Notebook: Trie map
 Notebook: Suffix trie
 Suffix trees
 Notebook: Suffix tree
 Suffix arrays
 Notebook: Binary search
 Notebook: Suffixarray binary search
 Notebook: Longest common prefix
 Notebook: From suffix tree to LCP/suffix array
 BurrowsWheeler Transform and FM Index
 Notebook: BurrowsWheeler Transform
 Notebook: Reversing the BWT
 Notebook: FM Index
 Indexing with substrings
 Sequence alignment
 Dynamic programming and edit distance
 Variations on edit distance
 Notebook: Approximate matching dynamic programming
 Notebook: Longest common subsequence (LCS)
 Global alignment
 Notebook: Global alignment
 Local alignment
 Notebook: Local alignment
 Dynamic programming in less time and space
 Indexassisted approximate matching and read alignment
 Notebook: Indexassisted pigeonhole principle
 Assembly
 Assembly & Shortest Common Superstring
 Notebook: Bruteforce SCS
 Notebook: Finding overlaps
 Notebook: Greedy SCS
 Overlap Layout Consensus assembly
 De Bruijn Graph assembly
 Notebook: Simple De Bruijn graph
 Notebook: De Bruijn graph
 Error correction
 Notebook: Error correction
 Scaffolding
 Assembly & Shortest Common Superstring
 Sequence models and classification

 Motivation: epigenetics and CpG islands
 Markov chains (v2, Dec 2017)
 Notebook: Markov chains
 Notebook: Highorder Markov chains
 Hidden Markov models
 Notebook: Hidden Markov Model
 Genes and gene finding
 File formats
 Miscellaneous

 Notebook: Radix sort
 Notebook: Min hashing
 Notebook: Minimizers
 Notebook: RepeatMasker
124 Comments
Ben – Thanks for the great illustrations in your BWT/FM and assembly slides. We are using them in my graduate subject at MIT. Job well done! David Gifford
Hi Ben, I’m using some of these slides in the Comp. Bio. course here at Stony Brook. Thanks for providing this resource; it’s really useful!
Hi Ben – I am using some of your slides in my computational genomics class at the University of Illinois at UrbanaChampaign. Thank you very much for the great resource! — Jian Ma
I have used some slides for an avolutionary genomics and genomics method class – thanks a lot!
Thanks so much for making this material available. I made use of the De Bruijn Graph code to have students interactively explore small De Bruijn Graphs, see https://github.com/lexnederbragt/INFBIOx121_fall2014_de_novo_assembly under ‘practicals’
Great slides, thanks for making them available. I am using some of the assembly slides in a genome assembly workshop organized by the informatics group in Research Computing at Harvard.
Hi Ben — thanks for the slides (and for TopHat). I’m using the de Bruijn graph slides for an Intro to Comp Bio course for CS undergraduates.
Thanks for posting teaching materials Ben. I am using some of your slides in an applied genomics course at New York University
Hi Ben, I’m using some of your slides in a a viral biodiversity course here at University of Brasilia Brazil. Thanks for sharing your teaching material. Fernando
Thanks so much for making this material public! I have adapted much of the material on the BW transform and the FM index (which you present in an incredibly lucid way!) for a lecture in my Genomics course at the Free University Berlin.
Thank you for your material!! I plan to use some of your slides for a part of the course Programming for Bioinformatics at University of Bologna.
Thank you for making your slides available Professor Langmead. Best concise description of de Bruijn graph assembly I have found. I am using them to develop an understanding of genome assemblers for a rotation project at Stanford.
I have found your lecture slides on the topic Edit Distance useful and decided to use it, partially or fully. I hope that the rest of the material on this page is also useful. Thank you so much for such a nice platform for the subject of algorithms. I am going to use this lecture during a course “Advance Analysis of Algorithms” at graduate level at University of Sargodha, Pakistan.
Hi Ben,
just downloaded them for personal use. Brilliant talk on FM and BWT!!
Hi, I used the De Bruin Graph Assembly presentation to help me understand the algorithm in my research. Thank you!
Thank you for providing such a wonderful resource! I am using your some of your lecture slides on de Bruijn Graph assembly in an Intro to Computational Biology graduate course at the University of Minnesota.
Thank you for making your slides available. They are very well informed and goes into immense detail. We are planning on using these slides, at reference De Brujin modeling for sequencing, for our bioinformatics presentation.
Thanks Ben for these nice slides. I will use some slides from the assembly slide deck for a bioinformatics course at Kansas State University.
Using figure as part of a informatics summer course at the University of Iowa — Thanks!
Taking online courses (edX MOOCs) in BioInformatics by professors at UC San Diego. This looks like a wealth of great supporting material
Hi Ben,
I use these to learn about bioinformatics myself, and also to teach others at Public Health England.
Thanks!
Phil
Thanks for the materials. I will use some of the slides for a computational genomics course at Uconn.
Hi Ben – Thanks so much for making this wonderful material public! I have used or adapted some slides for my computational genomics introductory class at the Universidad Autonoma de Madrid.
Awesome lectures with superawesome analogies. Please more advanced courses on Coursera or even a specialization on Computational Biology.
Thanks for making your slides / material public. I am training graduates in NGS specifically, and your material makes for wonderful references – along with the published work. Much appreciated.
Regards,
Thanks so much for making these slides available. I’m adapting some of the assembly slides for an intro bioinformatics class.
Introductory Bioinformatics elective @ CS Engineering, Amrita University
I adapted your notes on strings and matching to give a brief tutorial to members of my lab (MSK) – thanks.
Ben, thank you so much for making your slides public. I am studying the ones about BWT and FMIndex in addition to your videolectures in preparation for a presentation on Bowtie/Bowtie2 at a ‘NGS methods” seminar at LudwigMaximillian University, Munich.
Thanks for these – I’m using some bits and pieces in a seminar on highthroughput sequencing in microbiology at the MahidolOxford Research Unit in Bangkok, Thailand.
Dear Ben, thank you for great teaching material. I am using your slides in an NGS course at the University of Warsaw,
with best wishes,
Ewa Szczurek
Dear Ben, Thank you for sharing such a great teaching material with us. I am contenting several slides in a Computational Biology course at Upenn.
Best,
Zerry
Thanks! I’m using part of the materials in an Algorithms in Bioinformatics course at the University of Turku, Finland. –Filip
I am using your materials on de Bruijn graph algorithms for genome assembly in my undergraduate class (CS 173)
Hi Ben,
Thank you so much for sharing this nice teaching resource. I am using several slides in a Bioinformatics course at the Universitat Autònoma de Barcelona (degree in Genetics).
Best,
Sònia
Nice work, particularly when education becomes so important in this area.
I am using some slides for an “introduction to bioinformatics” course in the University of Texas GSBS program. Some problem definitions are easy enough for biology students to understand.
Thanks for the contribution, Ben!
Thank you for sharing. I’m using your material about hash tables for an exposition in a Bioinformatics class that I’m taking in The Université de Montreal .
Hi! I used some parts of your slides for a presentation that covered DNA sequencing/assembly/alignment, here at a local tech meetup in Uppsala, Sweden. Thanks!
Thank you for making these slides available! I am using some on de Bruijn graph approaches in my Evolution in Agriculture class at the University of Minnesota Duluth.
Hoping to use in a graduate course on Pattern Matching Algorithms.
Dear Ben,
Thank you very much for sharing your great teaching material. I am using some of your materials in Intro to Bioinformatics course at Saint Louis University.
Best wishes,
Ted
Thanks for sharing! I will be using some slides from the assembly part for a metagenomics course in Barcelona
Nice slides. I’m using some of the slides on assembly for a guest lecture at UC Berkeley.
Ben – Thanks so much for sharing. I’m adapting some of your slides for my computational biology class at Carleton College. Layla Oesper
Hi Ben, thanks for sharing your slides. I am using parts of your lectures and teaching materials for my Introduction to Genomics class at Princeton University. Mohamed
Hi Ben, awesome job. I’m using some of your slides about de Bruijn graphs and BWT for a genome assembly course at the UANL (Mexico). Many thanks.
Hey there, using your slides as a reference while I do my homework for Bioinformatics Algorithms at Harvard Extension School. Thanks much – DF
Hi Ben, I have taken some of your figures for teaching a BWT class. Thanks much for making this material available. Rayan
Fantastic materials. Using them to teach BMMB554 at Penn State
Hi, thanks for sharing your teaching materials. I am adapting some of the slides for Intro to Bioinformatics course at Okan University.
Hi Ben,
These slides are really great. I am giving a talk to the BIG (Bioinformatics Group) at MIT about Sailfish, kallisto and Salmon and would like to use a couple of these slides to get across the idea of a De Bruijn graph which are essential to kallisto. Thank you for making them available. De Bruijn graphs are not what a lot of biologists are very familiar with and these slides explain them very well.
Ben, thanks for posting these. I am using/adapting some of these for my GENE245 course on Compbio at Stanford.
Ben, thanks for sharing this. I used some of your stuff on indexes for teaching mapping in my Bioinformatics and Systems Biology course. Nice examples.
Ah, forgot to say, I’m at Cal State University, Monterey Bay
Thanks Ben, I grabbed a few slides on alignment and sequencing for background in my class – and directed students to your course next Fall if they wanted more.
Thank you for sharing your slides, Ben. I’ll be borrowing from them for a presentation at Brown University’s ASA DataFest this weekend.
Dear Ben, thanks for sharing the materials. We’re referencing them for our Data Science for Sequencing course at Univ of Washington. They’re really helpful! Best wishes.
Many thanks for the access to the materials, they helped me explain to my friends, classmates and peers about RNASequencing during a group presentation in the University of Puerto Rico Rio Piedras Campus.
Ben, thanks so much for making and publishing these materials! I grabbed some images from the sequence alignment section for a lecture I will be giving in Leiden University.
Thanks for these excellent slides Ben – I’m going to use some for CSC2417 at the University of Toronto this fall.
Thanks so much for sharing your slides and allowing us to use it. I’m using some of your slides on sequence assembly and alignments in my comparative genomics class taught at Louisiana State University, Baton Rouge.
I came across slides from your lectures while preparing for my own course. I teach an introductory genomics/bioinformatics course for graduate students in the college of Agriculture. I find the graphics in your slides extremely useful. Really great work and thank you for sharing.
Thank you for sharing your slides. The lectures are really clear and want to use some of the slides for a lecture in a Computational Methods in Genomics course at Augusta University.
Dear Ben,
thank you for sharing your slides. I will use some of them in the NGS data analysis course at University of Warsaw.
Thank you for sharing the material. I using them in the Bioinformatics course at Universidade de Brasília, Brazil.
I will be using your slides to study for my transcriptomics class at NYU. Thank you so much for sharing!
Thanks for the material – will use some genome assembly figures for teaching at the Cyprus Institute.
Thanks Ben, I am using your slides on string matching for a lecture at LMU Munich.
Thanks Ben, I am using your slides on bioinformatics course at University of Kansas
Dear Ben, I am using your slides on BWT and FM index for a lecture at Sabanci University. Thank you for sharing.
Dear Ben, thanks for your great slides: I am using them for the Data Mining course (3rd year) at the University of Bolzano, Italy
Thanks for not just allowing reuse but for generating great slides Ben! We’re using these in overviews on genome assemblies for our workshops at the University of Illinois UrbanaChampaign.
Thanks for sharing these slides. It helped in preparing my lectures for a similar course in UCDavis.
Thanks for the graphics.
Using a few of these for a Functional Genomics course at the University of Alberta.
These slides are awesome! I am going to use the slides on the BWT and FM index for a presentation in my student seminary course at the University of British Columbia.
Thanks for these wonderful materials, Ben! I am using pieces of some of your lectures in my courses at Clark University (Introduction to Bioinformatics, and The Genome Project).
Ben – Thanks for the great illustrations in your assembly slides. We are using some of them in my undergraduate NGS practical at Giessen University, Germany. Excellent job ! Franz Cemic
Thank you very much for creating this resource! I am using the BWTFM index material in my graduate bioinformatics in diagnostic genetics class @ MD Anderson Cancer Center.
Dear Sir, I would like to use the material in this web for my undergraduate class Computational Biology .
Thanks so much for your slides, Ben! I’m using them to teach epigenetics course @ MIPT, Russia
Thanks for all the material. I am using certain parts in my undergraduate thesis project at the University of Malta.
Hi Ben, I’m using a few of your YouTube lectures on sequencing in the tutorials of my course ‘Applied Cell Biology’. Thanks for sharing these highquality and accessible lectures!
Thanks, Ben. Great resources! I plan to use them as BWTFM index material for bioinformatics section in genomic class. @ China Agricultural University.
The teaching method and the material you have created are just wonderful. I am using parts of them in my course “Advanced bioinformatics” in Sharif University of Technology, Tehran, Iran. Thanks a million.
Hi Ben.. I am a PhD student and teaching a 3rd year undergraduate class about algorithms in next generation sequencing. I found your material extremely helpful and educational. Much appreciated
Hi Ben, I’m using some of these slides in the Genomics Master course at Liverpool University. Many thanks for providing this resource – it’s fantastic!
Hi Ben, using parts of your material on BWT and the FM Index in my course on Genomics and Transcriptomics Data Analysis at Stuttgart University, Germany. Thanks a lot!
Hi Ben, your materials are great! Using them for my bachelor’s thesis at University of Zagreb, Croatia, Faculty of Electrical Engineering and Computing. Thank you very much for making these accessible to the public!
Hi Ben, Thanks so much for sharing this material. These are excellent lectures and I am happy that I could use them in a course on Applied Bioinformatics at Heinrich Heine University Düsseldorf, Germany.
Dear Ben, I will be using your materials on the FM Index for my undergraduate research project titled “BurrowsWheeler Transformation and its Applications”, at the National University of Singapore. Thank you for sharing your teaching materials as they really helped develop my understanding and interests in the aforementioned topics! 🙂
Hi Ben, your materials are great! Using them for my research at University of Split, Croatia, Faculty of Electrical Engineering, Mechanical Engineering and Naval Architecture (FESB). Thanks for sharing these highquality and accessible lectures!
I’ve posted links to several of your lectures on genome assembly for use by students in my graduate course on Evolutionary Genomics at the University of Arizona. Thanks much for making these outstanding lectures public.
Thanks a lot for allowing use of your excellent materials in an M.Sc. level course in Evolutionary genomics at the University of Oulu, Finland
Thanks a lot, for these materials. I plan to use some of your slides for a Phylogenomics graduate course at Universidad del Valle
Hi Ben, Wonderful resources. I am using some of your lecture slides to teach a course at IIITDelhi.
Thanks! I plan to use part of the materials in an Algorithms in Bioinformatics undergraduate course at the ELTE Eötvös Loránd University, Budapest, Hungary. – Attila Kiss
Great material – many thanks! I am using the materials on BurrowsWheeler transforms for teaching a bioinformatics course at the University of Pretoria.
Thanks for sharing these great materials. I am going to use some info from the slide in my algorithm assignment from James Cook University.
Thanks for the great material. I am using it in a bioinformatics course for undegraduate students.
Superb materials, a major timesaver in teaching (so far) string algorithms, BWT, suffix arrays, de novo assembly. I plan to use more!
Really great slides I’m taking the “lego” example of SBS to teach undergrads a broad introduction of DNA sequencing and bioinformatics.
Using from University of Waterloo.
Using from University of Oxford. Really comprehensive slides!
Hi Ben, thanks for these great materials and making them public! I will be using some of your slides for Genome Informatics course at Belgrade School of Electrical Engineering (ETF), University of Belgrade.
Thank you for sharing this excellent material! I’m using the BW and FM index part for an undergraduate course at University of Rome (Tor Vergata).
Using read correction slides at UMass Amherst. Great explanations. Thank you!
Thanks Ben, I’m using some of these slides in a course at UCSC.
Dear Ben, thank you for sharing these great slides! I am using some of your slides in a course at Chalmers
Thanks so much for the use of your slides on assembly algorithms. I used them for a beginner genomics and informatics course at the University of Calgary.
Thank you for sharing these slides. They are very helpful. I am using some for an introductory lecture on sequence assembly at Iowa State.
Hi Ben, Thank you for sharing this excellent material. I will be using the edit distance slides and some of the strings and matching examples in my programming courses in python and Matlab at the Hebrew University of Jerusalem
Thanks for sharing such a wealth of materials. One of my colleagues at SLU pointed me your way. These are wonderfully helpful for a freshman level introductory course that includes a mix of computer science and biology students.
Hi Ben, I am using some of your slides in my computational genomics class at the University of Hong Kong. Thank you for the great resources.
Hi Ben,
I am using your slides in my bioinformatics class in TOBB University, Turkey. Thanks a lot,
Hey Ben, I will be using some of these slides for a bioinformatics lecture at the College of William and Mary. Thanks for sharing.
Thanks Ben for sharing your wonderful teaching material. I will be using some of your slides for Introduction to Genomics at National YangMing University, Taipei, Taiwan.
Hello Ben! Thank you for sharing your slides on de Bruijn graph representation. I am using them to guide a discussion in our “gene expression and R” course at the University of California, Merced.
Hello Ben, Thanks so much for these great efforts. I will be using some of your slides for BWT and FM index for a algorithm and bioinformatics lecture at the University of Taipei in a few days. Thanks for sharing.
Hi Ben, I am using some of your slides in my genomics and bioinformatics class at UC Davis. Thanks so much for posting them!
Hi Ben, Thanks so much for these slides, they are a great resource. I will be using them for Bioinformatics class at the University of Maryland.
I am using your slides to aid my presentation of the original Bowtie paper for the Computational Biology Algorithms course at Georgia Tech. Love them!
Dear Ben Langmead
I am using your presentation on de Bruijn graph assembly as extra material for an introductory course in bioinformatics for my genomics students at University of Chinese Academy of Science.
Thank you for making your materials available!
I am using your introductory slides as a reference in our course on Quantitative and Computational Biology in Gerstner Sloan Kettering Graduate School. This is a really great resource, thank you very much.
Thanks for sharing these great slides – I am using some of the images in our introduction to sequencing course