If You are New Here
Our Objectives
A Road Map for our Journey through the Transcriptomic Maze
Introductory Articles on Bioinformatics
A beginner’s guide to bioinformatics - part I
A beginner’s guide to bioinformatics - part II
Algorithms for Next-gen Sequence Analysis
Large Computer, Distributed Cluster or Amazon Cloud?
Must-have Tools for a Bioinformatician
On de Bruijn Graphs
How do sequencing errors affect de Bruijn graphs?
De Bruijn Graphs for Alternative Splicing and Repetitive Regions
A Drawback of de Bruijn Graph Approach
De Bruijn Graphs for Alternative Splicing and Repetitive Regions
Using Mate Pair Information in de Bruijn Graphs
Contrail - A de Bruijn Genome Assembler that uses Hadoop
Watching a de Brujin Graph Assembler in Action (Contrail)
Updating a de Bruijn Assembler Code for Color Space Data in Six Easy Steps
Optimizing Sequence Assemblies
Maximizing Utility of Available RAMs in K-mer World
K-mer Sizes for Genome Assembly
Partitioning Libraries to Fit Small RAM Size
K-mer distribution of a transcriptome
Transcriptome Assemblers
De Novo Transcriptome Assemblers - Oases, Trinity, etc.
De Novo Transcriptome Assemblers Oases, Trinity, etc. - II
De Novo Transcriptome Assemblers Oases, Trinity, etc. III
De Novo Transcriptome Assemblers Oases, Trinity, etc. IV
Explaining Output of Trinity Component - Inchworm
Output of Oases Transcriptome Assembler
R for Transcriptomics
Using R for Transcriptome Analysis - I
Comparison of data analysis packages
Hadoop
Using Hadoop for Transcriptomics - An Example to Get Started
Contrail - A de Bruijn Genome Assembler that uses Hadoop
Watching a de Brujin Graph Assembler in Action (Contrail)
Sequence Alignment Methods
Finding us in homolog.us - part II
Finding us in homolog.us III (Search Algorithm and Indexing)
Burrows Wheeler transform - Suffix Arrays and FM Index
SOLiD/Color Space
The Mathematics of Color Space Sequencing
Do de Bruijn Assemblers Work in Color Space?
Trinity and Contrail for Color Space
Updating a de Bruijn Assembler Code for Color Space Data in Six Easy Steps
NCBI GEO Database
A Bird’s Eye View of NCBI GEO Database
A Bird’s Eye View of NCBI GEO Database - II
Transcriptomic Research around the Globe
Where are the global hotbeds of transcriptomic research?
GEO and SRA - Quarterly Growth in Transcriptomic Research
