Lecture
slides
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Recommended
reading
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A brief introduction to genomes and
concepts in genomics. Genome structure. Genomic variation.
Week 1, Lecture 1
Week 1, Lectures 2-3
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EBI's
Introduction to Biology
JGI's
Introduction to Genomics
Rare
and common variants: twenty arguments, Greg Gibson, Nature Rev
Genet
Repetitive
DNA and next-generation sequencing: computational challenges and
solutions, Treangen and Salzberg, Nature Rev Genet.
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Genomic variation discovery,
microarrays and other genotyping platforms.
Week 2, Lecture 1
Week 2, Lectures 2-3
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Microarray
overview
NCBI's
microarray primer
Rabiner's
tutorial on HMMs
HMMseg
SCIMM
SCIMMkit
SCOUT
BirdSuite
ÇOKGEN
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Introduction to high throughput
sequencing (HTS). Different sequencing platforms, pyrosequencing,
sequencing by synthesis, sequencing by ligation, single molecule
sequencing. Upcoming platforms based on nanotechnology. Advantages
and disadvantages. Computational challanges in analyzing HTS data.
Week 3, Lecture 1
Weed 3, Lectures 2-3
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Sequencing
technologies - the next generation.
Computational
solutions to large-scale data management and analysis.
CRAMtools
If you are interested in the SCALCE paper, send me an email for a
preprint since it is not published yet.
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Read mapping. Burrows-Wheeler
Transform and Ferragina-Manzini index. Hash
based and BWT-FM based aligners.
Week 4, Lectures 1-2-3
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Comparison
of read mappers
MAQ
& mapping qualities
Bowtie and
BWT-FM
mrsFAST
and cache oblivious mapping
ZOOM!
and spaced seeds
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SNP and small indel discovery using
HTS. Haplotype resolution.
Week 5, Lecture 1
Week 5, Lectures 1-2
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GATK,
Samtools,
PyroBayes,
SNP
calling review by Nielsen et al.
SPLITREAD,
Dindel,
PHASE
Fosmid
based haplotype phasing
Phasing
using sequencing and fragment conflict graps
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Structural variation, copy number
variation, copy number polymorphism and segmental duplications.
Week 6, Lecture 1
Week 6, Lectures 2-3
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Review
on SV discovery & genotyping methods
1000
Genomes SV Companion
First algorithms:
Read
depth Read
Pair Split
Read
NGS versions
NGS
WSSD CNVnator
EWT
ExomeCNV
VariationHunter
VariationHunter2
BreakDancer
Pindel
NovelSeq
CNVer
GenomeSTRiP
BreakSeq
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Sequence assembly algorithms. De
Bruijn graphs for genome assembly. String graphs. Techniques and
shortcomings of assembly.
Week 7, Lecture 1
Week 7, Lectures 2-3
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Assembly
of large genomes
Assembly
algorithms for NGS
Lander-Waterman
statistics
Celera
Assembler Arachne
de
Bruijn Graphs Primer
Assembler
Comparison
Bloom
filter
Error correction: Quake
SHREC
ECHO
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De Bruijn graphs for genome
assembly.
Week 8, Lecture 1
Transcriptome analysis. Transcriptome assembly, alternative
splicing and fusion gene discovery.
Week 8, Lectures 2-3
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EULER
ABySS
Velvet
ALLPATHS-LG
Cortex
Ray
RNAseq
review 1
RNAseq
review 2
Transcriptome
assembly review
TopHat
Cufflinks
RPKM
Trans-ABySS
Scaffolding
with RNAseq
deFuse
Comrad
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Epigenetics. Methylation, histone
modification. Finding ``active'' genes using DNAseI
hypersensitivity assays.
Week 9, Lecture 1
Histone modification. RNA secondary structure prediction
Week 9, Lectures 2-3
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DNA
methylation review
BATMAN
BSMAP
Bismark
ChIP-seq
review
Segway
PeakSeq
Zuker&Stiegler
Mfold
ViennaRNA
RNAalifold
Zuker's RNA page
Hofacker's RNA
page
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RNA folding
Week 10, Lecture 1
RNA-RNA interactions, protein sequencing
Week 10, Lectures 2-3
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Densityfold
CONTRAfold
SCFG for
folding
PairFold
inteRNA
SEQUEST
SHERENGA
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