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

De Bruijn graphs - I

De Bruijn graphs - II

De Bruijn Graphs - III

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

Sharing a K-mer Story

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

Hadoop Example - FAQ

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

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

Data Compression Algorithms

Suffix Arrays

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


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Written by M. //