|A brief introduction to genomes and
concepts in genomics. Genome structure. Genomic variation.
Week 1, Lecture 1
Week 1, Lectures 2-3
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.
|Genomic variation discovery,
microarrays and other genotyping platforms.
Week 2, Lecture 1
Week 2, Lectures 2-3
NCBI's microarray primer
Rabiner's tutorial on HMMs
HMMseg SCIMM SCIMMkit SCOUT BirdSuite «OKGEN
|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
technologies - the next generation.
Computational solutions to large-scale data management and analysis.
If you are interested in the SCALCE paper, send me an email for a preprint since it is not published yet.
|Read mapping. Burrows-Wheeler
Transform and Ferragina-Manzini index. Hash
based and BWT-FM based aligners.
Week 4, Lectures 1-2-3
of read mappers
MAQ & mapping qualities
Bowtie and BWT-FM
mrsFAST and cache oblivious mapping
ZOOM! and spaced seeds
|SNP and small indel discovery using
HTS. Haplotype resolution.
Week 5, Lecture 1
Week 5, Lectures 1-2
SNP calling review by Nielsen et al.
SPLITREAD, Dindel, PHASE
Fosmid based haplotype phasing
Phasing using sequencing and fragment conflict graps
|Structural variation, copy number
variation, copy number polymorphism and segmental duplications.
Week 6, Lecture 1
Week 6, Lectures 2-3
on SV discovery & genotyping methods
1000 Genomes SV Companion
Read depth Read Pair Split Read
NGS WSSD CNVnator EWT
BreakDancer Pindel NovelSeq
CNVer GenomeSTRiP BreakSeq
|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
of large genomes
Assembly algorithms for NGS
Celera Assembler Arachne
de Bruijn Graphs Primer
Error correction: Quake SHREC ECHO
|De Bruijn graphs for genome
Week 8, Lecture 1
Transcriptome analysis. Transcriptome assembly, alternative splicing and fusion gene discovery.
Week 8, Lectures 2-3
RNAseq review 1
RNAseq review 2
Transcriptome assembly review
TopHat Cufflinks RPKM Trans-ABySS
Scaffolding with RNAseq
|Epigenetics. Methylation, histone
modification. Finding ``active'' genes using DNAseI
Week 9, Lecture 1
Histone modification. RNA secondary structure prediction
Week 9, Lectures 2-3
BATMAN BSMAP Bismark
Mfold ViennaRNA RNAalifold
Zuker's RNA page
Hofacker's RNA page
Week 10, Lecture 1
RNA-RNA interactions, protein sequencing
Week 10, Lectures 2-3