Канал: Ben Langmead

BWT for repetitive texts, part 3: Toehold lemma setup

BWT for repetitive texts, part 3: Toehold lemma setup

Suffix arrays: the suffix tree is hiding

Suffix arrays: the suffix tree is hiding

BWT for repetitive texts, part 2: Run-length FM index

BWT for repetitive texts, part 2: Run-length FM index

Suffix arrays: building

Suffix arrays: building

Suffix arrays: maximum skipping

Suffix arrays: maximum skipping

Suffix arrays: min LCP skipping

Suffix arrays: min LCP skipping

Suffix arrays: basic queries

Suffix arrays: basic queries

Suffix arrays: definition & size

Suffix arrays: definition & size

Matching statistics on the suffix tree

Matching statistics on the suffix tree

Suffix trees: matching statistics

Suffix trees: matching statistics

Suffix trees: suffix links

Suffix trees: suffix links

Suffix trees: basic queries

Suffix trees: basic queries

Suffix trees: building

Suffix trees: building

Suffix trees: definition & size

Suffix trees: definition & size

Suffix tries: size

Suffix tries: size

Suffix tries: introduction

Suffix tries: introduction

Tries

Tries

BWT for repetitive texts, part 1: Runs

BWT for repetitive texts, part 1: Runs

Wheeler graphs, part 5: Data structures

Wheeler graphs, part 5: Data structures

Wheeler graphs, part 4: Consecutivity

Wheeler graphs, part 4: Consecutivity

Wheeler graphs, part 3: Definition

Wheeler graphs, part 3: Definition

Wheeler graphs, part 2: BW order for graphs

Wheeler graphs, part 2: BW order for graphs

Wheeler graphs, part 1: substrings to paths

Wheeler graphs, part 1: substrings to paths

FM Index, part 2: efficient matching

FM Index, part 2: efficient matching

FM Index, part 1: efficient reversal

FM Index, part 1: efficient reversal

Wavelet trees, part 2

Wavelet trees, part 2

Wavelet trees, part 1

Wavelet trees, part 1

Clark's select

Clark's select

Burrows-Wheeler Transform, part 2

Burrows-Wheeler Transform, part 2

Burrows-Wheeler Transform, part 1

Burrows-Wheeler Transform, part 1

High order empirical entropy

High order empirical entropy

CountMin sketch, part 3

CountMin sketch, part 3

CountMin sketch, part 2: proving error bound

CountMin sketch, part 2: proving error bound

CountMin sketch, part 1

CountMin sketch, part 1

Markov's inequality

Markov's inequality

Similarity & MinHash

Similarity & MinHash

Cardinality part 2: proof & kth minimum value

Cardinality part 2: proof & kth minimum value

Cardinality part 1: the hat problem

Cardinality part 1: the hat problem

Universal hashing with a prime field

Universal hashing with a prime field

Universal hashing part 1: motivation

Universal hashing part 1: motivation

Coupon collector and more Bloom filters

Coupon collector and more Bloom filters

Bloom filters, part 2

Bloom filters, part 2

Bloom filters, part 1

Bloom filters, part 1

Hashes & randomness

Hashes & randomness

Hash tables & probability, part 2

Hash tables & probability, part 2

Hash tables & probability, part 1

Hash tables & probability, part 1

Randomness & independence

Randomness & independence

Entropy & coding

Entropy & coding

Intro: Indexing

Intro: Indexing

Jacobson's rank

Jacobson's rank

Bitvectors and rank/select

Bitvectors and rank/select

Dashing: fast & accurate genomic distances with HyperLogLog

Dashing: fast & accurate genomic distances with HyperLogLog

ADS1: Meet the family: global and local alignment

ADS1: Meet the family: global and local alignment

ADS1: Using dynamic programming for edit distance

ADS1: Using dynamic programming for edit distance

ADS1: Using dynamic programming for edit distance

ADS1: Using dynamic programming for edit distance

ADS1: Genome indexes used in research

ADS1: Genome indexes used in research

ADS1: Variations on k-mer indexes

ADS1: Variations on k-mer indexes

ADS1: Solving the edit distance problem

ADS1: Solving the edit distance problem

ADS1: The future is long?

ADS1: The future is long?

ADS1: Assemblers in practice

ADS1: Assemblers in practice

ADS1: Computer science and life science

ADS1: Computer science and life science

ADS1: De Bruijn graphs and Eulerian walks

ADS1: De Bruijn graphs and Eulerian walks

ADS1: When Eulerian walks go wrong

ADS1: When Eulerian walks go wrong

ADS1: Practical: Implementing greedy shortest common superstring

ADS1: Practical: Implementing greedy shortest common superstring

ADS1: Practical: Building a De Bruijn graph

ADS1: Practical: Building a De Bruijn graph

ADS1: Third law of assembly: repeats are bad

ADS1: Third law of assembly: repeats are bad

ADS1: Greedy shortest common superstring

ADS1: Greedy shortest common superstring

ADS1: The shortest common superstring problem

ADS1: The shortest common superstring problem

ADS1: Practical: Implementing shortest common superstring

ADS1: Practical: Implementing shortest common superstring

ADS1: Overlap graphs

ADS1: Overlap graphs

ADS1: Practical: Finding and representing all overlaps

ADS1: Practical: Finding and representing all overlaps

ADS1: Practical: Overlaps between pairs of reads

ADS1: Practical: Overlaps between pairs of reads

ADS1: First and second laws of assembly

ADS1: First and second laws of assembly

ADS1: Assembly: working from scratch

ADS1: Assembly: working from scratch

ADS1: Read alignment in the field

ADS1: Read alignment in the field

ADS1: Practical: Implementing global alignment

ADS1: Practical: Implementing global alignment

ADS1: Meet the family: global and local alignment

ADS1: Meet the family: global and local alignment

ADS1: Practical: Implementing dynamic programming for edit distance

ADS1: Practical: Implementing dynamic programming for edit distance

ADS1: Diversion: Repetitive elements

ADS1: Diversion: Repetitive elements

ADS1: Practical: Matching real reads

ADS1: Practical: Matching real reads

ADS1: Naive exact matching

ADS1: Naive exact matching

ADS1: Practical: Implementing the pigeonhole principle

ADS1: Practical: Implementing the pigeonhole principle

ADS1: Edit distance for approximate matching

ADS1: Edit distance for approximate matching

ADS1: Pigeonhole principle

ADS1: Pigeonhole principle

ADS1: Hash tables for indexing

ADS1: Hash tables for indexing

ADS1: Approximate matching, Hamming and edit distance

ADS1: Approximate matching, Hamming and edit distance

ADS1: Practical: Implementing a k-mer index

ADS1: Practical: Implementing a k-mer index

ADS1: Practical: Implementing Boyer-Moore

ADS1: Practical: Implementing Boyer-Moore

ADS1: Ordered structures for indexing

ADS1: Ordered structures for indexing

ADS1: Indexing and k-mer indexes

ADS1: Indexing and k-mer indexes

ADS1: Preprocessing

ADS1: Preprocessing

ADS1: Boyer-Moore: putting it all together

ADS1: Boyer-Moore: putting it all together

ADS1: Boyer-Moore basics

ADS1: Boyer-Moore basics

ADS1: Naive exact matching

ADS1: Naive exact matching

ADS1: Practical: Matching artificial reads

ADS1: Practical: Matching artificial reads

ADS1: Practical: Analyzing reads by position

ADS1: Practical: Analyzing reads by position

ADS1: Practical: Working with sequencing reads

ADS1: Practical: Working with sequencing reads

ADS1: Practical: Downloading and reading a genome

ADS1: Practical: Downloading and reading a genome

ADS1: Practical: Manipulating DNA strings

ADS1: Practical: Manipulating DNA strings

ADS1: Practical: String basics

ADS1: Practical: String basics

ADS1: Sequencing by Synthesis

ADS1: Sequencing by Synthesis

ADS1: Why study DNA sequencing and computational genomics?

ADS1: Why study DNA sequencing and computational genomics?

ADS1: DNA: the molecule, the string

ADS1: DNA: the molecule, the string

ADS1: How DNA is copied

ADS1: How DNA is copied

ADS1: Read alignment and why it's hard

ADS1: Read alignment and why it's hard

ADS1: Base calling and sequencing errors

ADS1: Base calling and sequencing errors

ADS1: Sequencers give pieces to genomic puzzles

ADS1: Sequencers give pieces to genomic puzzles

ADS1: DNA sequencing past and present

ADS1: DNA sequencing past and present

ADS1: String definitions and Python syntax

ADS1: String definitions and Python syntax

ADS1: Reads in FASTQ format

ADS1: Reads in FASTQ format

FM Index

FM Index

Burrows-Wheeler Transform

Burrows-Wheeler Transform

Suffix tries and trees

Suffix tries and trees